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sequences (#323)\r\n- Reuse input FASTQ buffers to reduce memory allocations (#325)\r\n- Reuse compression streams and buffers for isa-l and libdeflate (#327)\r\n- Use look-up tables to check and normalize nucleotides (#328)\r\n- Optimized Mott trimming by performing calculations using integers (#360)\r\n- Close and flush output files using multiple threads (#362)\r\n- Specialize FASTQ validation/conversion functions for each input format 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v3 is a major revision of AdapterRemoval v2 that aims to simplify\r\nusage via sensible default settings. AdapterRemoval v3 expands the range of\r\nfeatures available in v2, as well as greatly increasing throughput.\r\n\r\nSee the documentation for a detailed guide of how to migrate from earlier\r\nversions of AdapterRemoval:\r\n<https://adapterremoval.readthedocs.io/en/v3.0.0/migrating.html>\r\n\r\nSee the changelog for a full list of changes since AdapterRemoval v2.3.x:\r\n<https://github.com/MikkelSchubert/adapterremoval/blob/v3.0.0/CHANGES.md>\r\n\r\n### Added\r\n\r\n- \\[**BREAKING**\\] The appropriate adapter sequences for trimming are now\r\n  selected automatically by default (configurable via `--adapter-selection` or\r\n  by manually setting adapter sequences), with configurable fallback strategies\r\n  for when detection fails (#196)\r\n- \\[**BREAKING**\\] Added `--normalize-mate-separator` option to allow optional\r\n  normalization of the mate separator character. This is no longer enabled by\r\n  default (#221)\r\n- \\[**BREAKING**\\] Automatically enable poly-G trimming of Illumina data, when\r\n  this can be identified. This behavior can be disabled/overridden (#225)\r\n- It is now possible to build AdapterRemoval for Windows using an MSYS2/UCRT64\r\n  environment. Static binaries be executed outside this environment (#237)\r\n- \\[**BREAKING**\\] Added `--max-ns-fraction 0.05` as a default filter, filtering\r\n  any trimmed read that contains more than 5% uncalled bases.\r\n- Support quality trimming/merging under the assumption that input data does not\r\n  contain adapter sequences. This is intended for already trimmed input (#171)\r\n- Attempting to use deprecated or removed options now displays a message\r\n  describing the change and, if possible, how to migrate (#181, #182)\r\n- Support explicitly undefined/unknown adapters for trimming of PE reads (#194)\r\n- Embedded the current git-checksum in the version string (#199)\r\n- Report the number of bases corrected or masked during merging (#201)\r\n- The optimal SIMD instruction sets is now selected based on the dataset (#175)\r\n- Added checks for all possible combinations of overlapping input/output files,\r\n  and checks for inconsistent paths that can lead to unexpected results (#244)\r\n- Added feature flags for building docs, the man-page, and using mimalloc (#263)\r\n\r\n### Changed\r\n\r\n- \\[**BREAKING**\\] Made `--compression-level 1` use libdeflate level 1\r\n  compression and `--compression-level 2` use libdeflate level 2 compression.\r\n  This removes an extra compression level compared to other software (#209)\r\n- \\[**BREAKING**\\] Revert change of `--trim-mott-rate` to `--trim-mott-quality`,\r\n  to more closely match other tools supporting mott trimming (#211).\r\n- \\[**BREAKING**\\] Reworked poly-x trimming algorithm to improve sensitivity, by\r\n  finding the longest valid alignment instead of the first valid alignment, at\r\n  the cost of slightly lower throughput (#224)\r\n- \\[**BREAKING**\\] Output files for discarded and singleton reads are now\r\n  created unconditionally, to simplify pipelines. This reverts a change in\r\n  alpha3 (#229)\r\n- \\[**BREAKING**\\] Options `--trim-ns` and `--trim-qualities` are now always\r\n  enabled when performing quality based trimming (#252)\r\n- \\[**BREAKING**\\] `--merge-strategy` no longer implies `--merge` (#265)\r\n- \\[**BREAKING**\\] Renamed `--min-adapter-overlap` to `--min-overlap`, and apply\r\n  this option to PE alignments, with a default value corresponding to\r\n  `--merge-treshold`. This mostly applies to trimming with unspecified adapters\r\n  or were the known adapter sequences are very short (#305)\r\n- Applied `--min-overlap` to both SE and PE alignments\r\n- Use min-overlap as filter when building consensus adapters\r\n- Set PE specific default for --min-overlap\r\n- Optimized PE aignments using NEON for ~20% higher throughput (#152)\r\n- `--mismatch-rate` rate arguments greater than 0.5 are deprecated, and the\r\n  default value has been changed from 6 (corresponding to 1/6) to 0.1667 (#189)\r\n- Renamed `--adapter-list` and `-barcode-list` to `--*-table`, to reflect the\r\n  expected content of these files. The old names supported but deprecated (#191)\r\n- Warn about and skip duplicate adapter sequences. This should have no effect on\r\n  results, but increases throughput (#192)\r\n- AdapterRemoval now has experimental support for link-time optimization (LTO).\r\n  This can be turned on via the build-time option `make LTO=true` (#227).\r\n- Always use libdeflate's crc32, for a small speedup on non-Intel systems (#208)\r\n- The `make` targets `static` and `static-container`no longer require all\r\n  dependencies to be installed. Instead, only Docker/Podman is required (#233)\r\n\r\n### Fixed\r\n\r\n- Edge case in SE alignments that would trigger asserts due to pointless\r\n  alignments when multiple adapters were specified (#147)\r\n- Checks for sample-name 'unidentified' are now case-insensitive, to prevent the\r\n  use of a reserved filename on case-insensitive filesystems (#179)\r\n- Edge case in duplication estimates could result in less exact estimates (#185)\r\n- Duplication statistics for mate 2 are no longer written in SE mode (#186)\r\n- Human readable timestamps are now used in the HTML report (#190)\r\n- FASTQ parsing errors spanning multiple files now lists those files (#205)\r\n- Fixed static (musl) builds with link-time optimization (LTO) enabled (#206)\r\n- Fixed build on older system with outdated compilers or meson versions (#213)\r\n- Fixed mate separator being written to SE SAM/BAM output (#218)\r\n- Fixed some invalid Solexa scores resulting in an unhandled exception instead\r\n  of a meaningful error message (#230)\r\n- The percent of identified insert sizes now only consider identified reads when\r\n  demultiplexing is enabled, as unidentified reads are not aligned (#231)\r\n- Fixed support for `-` to mean `STDIN` for `--in-file1` and `--in-file2` (#245)\r\n- Fixed some bases being skipped in calculation of read complexity (#253)\r\n- Fixed possible race condition if file handles were exhausted (#259)\r\n- Fixed possible overflow when merging very high-quality bases using the\r\n  `additive` read-merging strategy (#264)\r\n- Fixed output when writing BAM records with ambiguous bases (N) (#275)\r\n- Fixed command-line parsing errors not respecting `--log-colors` (#294)\r\n- Fixed Phred scores for consensus adapters being rounded down (#297)\r\n- Fixed passthrough of UTF-8 filenames in JSON output (#298)","reactions":{"url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/317667198/reactions","total_count":1,"+1":0,"-1":0,"laugh":0,"hooray":1,"confused":0,"heart":0,"rocket":0,"eyes":0}},{"url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/219600347","assets_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/219600347/assets","upload_url":"https://uploads.github.com/repos/MikkelSchubert/adapterremoval/releases/219600347/assets{?name,label}","html_url":"https://github.com/MikkelSchubert/adapterremoval/releases/tag/v3.0.0-alpha3","id":219600347,"author":{"login":"MikkelSchubert","id":2411627,"node_id":"MDQ6VXNlcjI0MTE2Mjc=","avatar_url":"https://avatars.githubusercontent.com/u/2411627?v=4","gravatar_id":"","url":"https://api.github.com/users/MikkelSchubert","html_url":"https://github.com/MikkelSchubert","followers_url":"https://api.github.com/users/MikkelSchubert/followers","following_url":"https://api.github.com/users/MikkelSchubert/following{/other_user}","gists_url":"https://api.github.com/users/MikkelSchubert/gists{/gist_id}","starred_url":"https://api.github.com/users/MikkelSchubert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MikkelSchubert/subscriptions","organizations_url":"https://api.github.com/users/MikkelSchubert/orgs","repos_url":"https://api.github.com/users/MikkelSchubert/repos","events_url":"https://api.github.com/users/MikkelSchubert/events{/privacy}","received_events_url":"https://api.github.com/users/MikkelSchubert/received_events","type":"User","user_view_type":"public","site_admin":false},"node_id":"RE_kwDOAS6r184NFtXb","tag_name":"v3.0.0-alpha3","target_commitish":"master","name":"AdapterRemoval 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is the third alpha release of AdapterRemoval v3. As with the previous alpha\r\nreleases, changes that affect how AdapterRemoval is used (e.g. by removing\r\noptions) or that result in different output compared to previous versions are\r\nmarked with the label \"[**BREAKING**]\".\r\n\r\nAdapterRemoval now uses `meson` for its build process, and `meson` is therefore\r\na build-time requirement. A `Makefile` is still provided to simplify setting up\r\nand running the build. See the installation instructions in the documentation\r\nfor more information.\r\n\r\nMajor changes include support for hardware accelerated alignments using NEON on\r\nmodern Apple hardware, support for samples being identified by multiple\r\nbarcodes, support for handling barcodes in that may ligate in different\r\norientations, improved support for SAM/BAM output, and (optional) duplication\r\nplot in HTML report.\r\n\r\nFor more information, see\r\nhttps://github.com/MikkelSchubert/adapterremoval/blob/v3.0.0-alpha3/README-v3.md\r\n\r\n### Added\r\n\r\n- Multiple barcodes/barcode pairs may now be used to identify the same sample,\r\n  via the `--multiple-barcodes` flag. The number of hits per barcode/barcode\r\n  pair is reported in the HTML/JSON reports.\r\n- Added support for handling barcodes that may ligate in different orientations\r\n  (via `--barcode-orientation`) and for normalizing the orientation of merged\r\n  reads (via `--normalize-orientation`).\r\n- The `--use-colors` parameter may now be used to controls color output.\r\n  Options are auto (default; enabled when run interactively), always, or never.\r\n- The title of the HTML report can now be set via `--report-title`.\r\n- Input files are now checked for duplicate filenames, in order to help\r\n  prevents accidental data duplication.\r\n- Alignments are now accelerated on Apple hardware using NEON instructions, for\r\n  a roughly 3-fold increase in throughput.\r\n- A duplication plot is now included in the HTML report if this is enabled,\r\n  instead of only being reported in the JSON file.\r\n\r\n### Changed\r\n\r\n- [**BREAKING**] Changed  `CO` tags for read-groups in SAM/BAM files to `DS`\r\n  (description) tags, in order to match the specification.\r\n- [**BREAKING**] A number of changes have been made to the JSON report layout,\r\n  including the moving, removal, and addition of sections. The layout is\r\n  described in `schema.json`.\r\n- [**BREAKING**] The minimum allowed/default value for `--min-adapter-overlap`\r\n  was set to 1. In practice this has no effect, since length 0 alignments were\r\n  never considered, but may break scripts running AdapterRemoval.\r\n- [**BREAKING**] Drop support for raw error-rates to `--trim-mott-rate`, which\r\n  was renamed to `--trim-mott-quality` to match other trimming options.\r\n- [**BREAKING**] SAM/BAM output is now combined into a single file by default,\r\n  including discarded reads. This can be overridden by setting the individual\r\n  `--out-*` options.\r\n- [**BREAKING**] Dropped `PG` tag from read-groups/records in SAM/BAM output.\r\n- [**BREAKING**] Dropped (minimal) read-groups for SAM/BAM output. If desired,\r\n  read-group information can be added with `--read-group`.\r\n- [**BREAKING**] The `--report-duplication` option now supports k/m/g suffixes,\r\n  and defaults to `100k` if used without an explicit value.\r\n- [**BREAKING**] The `--read-group` option no longer attempts to unescape\r\n  special characters. Instead, tags must be separated using embedded tabs\r\n  (`--read-group $'ID:A\\tSM:B'`) or provided as individual arguments\r\n  (`--read-group 'ID:A' 'SM:B'`).\r\n- Improved checks for conflicting command-line options.\r\n- Barcodes are now recorded in FASTQ headers demultiplexing without trimming.\r\n- The `$schema` URL is now included in the JSON report\r\n- Makefile features are now enabled/disable with `true`/`false` instead of\r\n  `yes`/`no`.\r\n- Vega-lite is now loaded in the background, when opening the HTML reports,\r\n  making the report readable before Vega-lite has loaded.\r\n- Optimized alignments involving multiple possible adapter sequences, by only\r\n  once performing the alignments that involve no adapter sequences.\r\n- Optimized alignments involving multiple possible adapter sequences, by\r\n  sorting the list of adapter sequences by hits. This increasing the odds that\r\n  a good alignment is found early so that worse alignments can be skipped.\r\n- The old Makefile was replaced with the Meson build system, but a wrapper\r\n  Makefile is still provided/used as a convenience for setting the recommended\r\n  build options.\r\n- A number of small improvements were made to the `--help` text.\r\n- Improved error messages when mismatching (paired) read names are detected.\r\n- Singleton reads are now included in the overall summary statistics in\r\n  JSON/HTML reports.\r\n- Hardening flags are now enabled by default during compilation. This comes with\r\n  a small performance cost, but most distros are also expected to enable similar\r\n  flags by default.\r\n\r\n### Fixed\r\n\r\n- NA values were being written with '%' or 'bp' suffixes in HTML report.\r\n- Some plots were omitted for merged reads in HTML report.\r\n- Mate 2 adapters were reverse-complemented in JSON report when demultiplexing.\r\n- SAM/BAM headers were not being written in demultiplexing mode.\r\n- Mate 1/2 statistics were sampled independently, and thus potentially not\r\n  derived from the same read pairs.\r\n- The JSON/HTML reports would give different time-stamps for the run, since one\r\n  gave the start time and the other the end time. Now start time is always used.\r\n- Fixed failure when reading paired FASTQ files where read lengths differed\r\n  between the two files\r\n- Fixed report files and unidentified reads getting additional suffixes when\r\n  filenames were specified manually during demultiplexing.\r\n- Fixed `/dev/null` being listed as the path for some files when demultiplexing,\r\n  and these outputs were disabled.\r\n- Reverted the removal of support for '.' as equivalent to 'N' in FASTQ reads.\r\n  This is found in some older data-sets (#112).\r\n- Fixed misleading IO error messages, that would include descriptions of\r\n  unrelated errors in some cases."},{"url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/171792907","assets_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/171792907/assets","upload_url":"https://uploads.github.com/repos/MikkelSchubert/adapterremoval/releases/171792907/assets{?name,label}","html_url":"https://github.com/MikkelSchubert/adapterremoval/releases/tag/v2.3.4","id":171792907,"author":{"login":"MikkelSchubert","id":2411627,"node_id":"MDQ6VXNlcjI0MTE2Mjc=","avatar_url":"https://avatars.githubusercontent.com/u/2411627?v=4","gravatar_id":"","url":"https://api.github.com/users/MikkelSchubert","html_url":"https://github.com/MikkelSchubert","followers_url":"https://api.github.com/users/MikkelSchubert/followers","following_url":"https://api.github.com/users/MikkelSchubert/following{/other_user}","gists_url":"https://api.github.com/users/MikkelSchubert/gists{/gist_id}","starred_url":"https://api.github.com/users/MikkelSchubert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MikkelSchubert/subscriptions","organizations_url":"https://api.github.com/users/MikkelSchubert/orgs","repos_url":"https://api.github.com/users/MikkelSchubert/repos","events_url":"https://api.github.com/users/MikkelSchubert/events{/privacy}","received_events_url":"https://api.github.com/users/MikkelSchubert/received_events","type":"User","user_view_type":"public","site_admin":false},"node_id":"RE_kwDOAS6r184KPVoL","tag_name":"v2.3.4","target_commitish":"master","name":"AdapterRemoval v2.3.4","draft":false,"immutable":false,"prerelease":false,"created_at":"2024-08-24T15:18:17Z","updated_at":"2024-08-24T15:25:08Z","published_at":"2024-08-24T15:25:08Z","assets":[],"tarball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/tarball/v2.3.4","zipball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/zipball/v2.3.4","body":"This release adds a new couple of command-line options for handling non-ACGTN\r\nbases in FASTQ data and back-ports a few minor fixes from the development\r\nbranch.\r\n\r\n### Added\r\n\r\n- Added support for converting Uracils (U) in input data to Thymine (T) via the\r\n  `--convert-uracils` flag.\r\n- Added support for replacing IUPAC-encoded degenerate bases with Ns via the\r\n  `--mask-degenerate-bases` flag.\r\n- Added DESTDIR support to `make install`.\r\n\r\n### Fixed\r\n\r\n- Improved progress timer accuracy, so updates occur closer to every 1M reads.\r\n\r\n### Changed\r\n\r\n- Minor improvements to `--help` text and documentation."},{"url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/171082251","assets_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/171082251/assets","upload_url":"https://uploads.github.com/repos/MikkelSchubert/adapterremoval/releases/171082251/assets{?name,label}","html_url":"https://github.com/MikkelSchubert/adapterremoval/releases/tag/v3.0.0-alpha2","id":171082251,"author":{"login":"MikkelSchubert","id":2411627,"node_id":"MDQ6VXNlcjI0MTE2Mjc=","avatar_url":"https://avatars.githubusercontent.com/u/2411627?v=4","gravatar_id":"","url":"https://api.github.com/users/MikkelSchubert","html_url":"https://github.com/MikkelSchubert","followers_url":"https://api.github.com/users/MikkelSchubert/followers","following_url":"https://api.github.com/users/MikkelSchubert/following{/other_user}","gists_url":"https://api.github.com/users/MikkelSchubert/gists{/gist_id}","starred_url":"https://api.github.com/users/MikkelSchubert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MikkelSchubert/subscriptions","organizations_url":"https://api.github.com/users/MikkelSchubert/orgs","repos_url":"https://api.github.com/users/MikkelSchubert/repos","events_url":"https://api.github.com/users/MikkelSchubert/events{/privacy}","received_events_url":"https://api.github.com/users/MikkelSchubert/received_events","type":"User","user_view_type":"public","site_admin":false},"node_id":"RE_kwDOAS6r184KMoIL","tag_name":"v3.0.0-alpha2","target_commitish":"master","name":"AdapterRemoval 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is the second alpha release of AdapterRemoval v3. It is the intention that\r\na third alpha release, or the final 3.0 release, will follow within the next\r\ncouple of months.\r\n\r\nAs with alpha 1, changes that affect how AdapterRemoval is used (e.g. by\r\nremoving options) or that result in different output compared to AdapterRemoval\r\nv2 are marked with the label \"[**BREAKING**]\".\r\n\r\nIn addition to changes listed below, this release includes increased throughput\r\nthanks to improved parallelization of various steps in internal pipeline,\r\nsupport for AVX512 and general improvements to the SIMD alignment algorithms,\r\nloop unrolling of non-SIMD alignments to significantly increase throughput when\r\nSIMD is not available, and a significant decrease in the number of allocations\r\nto decrease overhead.\r\n\r\nThis release requires a compiler with support for c++17 and libdeflate is now a\r\nmandatory dependency.\r\n\r\nDraft documentation is available [here](https://adapterremoval.readthedocs.io/en/v3.0.0-alpha2/) and a pre-compiled binary for x86-64\r\nLinux systems is attached below.\r\n\r\n### Added\r\n\r\n- Added support for converting (U)racils in input data to T(hymine) via the\r\n  `--convert-uracils` flag.\r\n- Added support for replacing IUPAC-encoded degenerate bases with Ns via the\r\n  `--mask-degenerate-bases` flag.\r\n- Added support for writing output in SAM/BAM formats, with optional\r\n  user-supplied read-group information.\r\n- Added support for alignments using AVX512 instructions. AVX512 support only\r\n  available when AdapterRemoval is compiled with GCC v11+ or Clang v8+.\r\n- Added support selecting output file formats via the file extension and via\r\n  the `--out-format` option. A corresponding option, `--stdout-format` was\r\n  added to select the format for data written to STDOUT.\r\n- Added support for reading from STDIN or writing to STDOUT when '-' is used as\r\n  the filename, as an alternative to using `/dev/stdin` or `/dev/stdout`.\r\n- Added dedicated threads solely for writing output data. This allows compute\r\n  threads to work at full capacity, as long as the destination can consume\r\n  written data fast enough. This may result in CPU utilization exceeding\r\n  `--threads` by a couple of percent.\r\n- Added support for setting DESTDIR when running `make install`.\r\n- Added `--licenses` flag for displaying licenses of 3rd party code used by /\r\n  incorporated into AdapterRemoval.\r\n- Added `--simd` option allowing the user to select the specific SIMD\r\n  instruction set they wish to use.\r\n- Added `Containerfile` for building static binaries using alpine/musl.\r\n\r\n### Changed\r\n\r\n- [**BREAKING**] Changed the default `--mm`/`--mismatch-rate` from 1/3 to 1/6,\r\n  in order to decrease the false positive rate, in particular for read merging.\r\n- [**BREAKING**] Default to writing gzip-compressed FASTQ files; output written\r\n  to STDOUT is uncompressed by default.\r\n- [**BREAKING**] Discarded reads are no longer saved by default.\r\n- [**BREAKING**] Output files for discarded reads and singleton (orphan)\r\n  paired-end reads are only created if filtering is enabled.\r\n- [**BREAKING**] The `--basename` / `--out-prefix` no longer defaults to\r\n  `your_output`. Instead the user is required to set at least one `--out-*`\r\n  option.\r\n- [**BREAKING**] Merged `--identify-adapters` and `--report-only` commands. The\r\n  adapter sequence is presently only reported in the HTML report, but will be\r\n  added to the JSON report following some planned changes.\r\n- [**BREAKING**] Reverted `--min-complexity` being enabled by default.\r\n- Increased the default ``--threads`` value to 2.\r\n- A number of command-line options were renamed for consistency; use of the old\r\n  names is still supported, but will trigger a warning message.\r\n- Re-organized compression: level 1 is streamed using isa-l, while levels 2-13\r\n  correspond to libdeflate levels 1 to 12.\r\n- Changed the default compression level to 5 on the new scale (libdeflate level\r\n  4); this results in a ~40% increase in throughput at the cost of roughly ~3%\r\n  larger output files.\r\n- Setting an `--out-*` option in demultiplexing mode overrides the basename /\r\n  prefix for that specific output type.\r\n- Add smoothing to GC values calculated for the GC content curve, to account\r\n  for the fact that possible GC% values are unevenly distributed depending on\r\n  the read length.\r\n\r\n### Removed\r\n\r\nThe following changes are all [**BREAKING**] as described above:\r\n\r\n- Removed support for original merging algorithm has been removed. The\r\n  `--merge-strategy additive` method produces very similar, but slightly more\r\n  conservative scores.\r\n- Removed the ability to randomly sample a base if no best base could be\r\n  selected in case of mismatches. Such bases are now changed to `N`, while both\r\n  methods assign a Phred score of 0 (`!`).\r\n"},{"url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/82306102","assets_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/82306102/assets","upload_url":"https://uploads.github.com/repos/MikkelSchubert/adapterremoval/releases/82306102/assets{?name,label}","html_url":"https://github.com/MikkelSchubert/adapterremoval/releases/tag/v3.0.0-alpha1","id":82306102,"author":{"login":"MikkelSchubert","id":2411627,"node_id":"MDQ6VXNlcjI0MTE2Mjc=","avatar_url":"https://avatars.githubusercontent.com/u/2411627?v=4","gravatar_id":"","url":"https://api.github.com/users/MikkelSchubert","html_url":"https://github.com/MikkelSchubert","followers_url":"https://api.github.com/users/MikkelSchubert/followers","following_url":"https://api.github.com/users/MikkelSchubert/following{/other_user}","gists_url":"https://api.github.com/users/MikkelSchubert/gists{/gist_id}","starred_url":"https://api.github.com/users/MikkelSchubert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MikkelSchubert/subscriptions","organizations_url":"https://api.github.com/users/MikkelSchubert/orgs","repos_url":"https://api.github.com/users/MikkelSchubert/repos","events_url":"https://api.github.com/users/MikkelSchubert/events{/privacy}","received_events_url":"https://api.github.com/users/MikkelSchubert/received_events","type":"User","user_view_type":"public","site_admin":false},"node_id":"RE_kwDOAS6r184E5-Q2","tag_name":"v3.0.0-alpha1","target_commitish":"master","name":"AdapterRemoval v3.0.0-alpha1","draft":false,"immutable":false,"prerelease":true,"created_at":"2022-11-07T18:46:39Z","updated_at":"2022-11-07T19:07:43Z","published_at":"2022-11-07T19:07:43Z","assets":[{"url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/assets/83783233","id":83783233,"node_id":"RA_kwDOAS6r184E_m5B","name":"adapterremoval-3.0.0-alpha1-linux64.tar.gz","label":null,"uploader":{"login":"MikkelSchubert","id":2411627,"node_id":"MDQ6VXNlcjI0MTE2Mjc=","avatar_url":"https://avatars.githubusercontent.com/u/2411627?v=4","gravatar_id":"","url":"https://api.github.com/users/MikkelSchubert","html_url":"https://github.com/MikkelSchubert","followers_url":"https://api.github.com/users/MikkelSchubert/followers","following_url":"https://api.github.com/users/MikkelSchubert/following{/other_user}","gists_url":"https://api.github.com/users/MikkelSchubert/gists{/gist_id}","starred_url":"https://api.github.com/users/MikkelSchubert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MikkelSchubert/subscriptions","organizations_url":"https://api.github.com/users/MikkelSchubert/orgs","repos_url":"https://api.github.com/users/MikkelSchubert/repos","events_url":"https://api.github.com/users/MikkelSchubert/events{/privacy}","received_events_url":"https://api.github.com/users/MikkelSchubert/received_events","type":"User","user_view_type":"public","site_admin":false},"content_type":"application/gzip","state":"uploaded","size":1359482,"digest":null,"download_count":38,"created_at":"2022-11-07T19:04:21Z","updated_at":"2022-11-07T19:04:25Z","browser_download_url":"https://github.com/MikkelSchubert/adapterremoval/releases/download/v3.0.0-alpha1/adapterremoval-3.0.0-alpha1-linux64.tar.gz"}],"tarball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/tarball/v3.0.0-alpha1","zipball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/zipball/v3.0.0-alpha1","body":"\r\nThis is the first alpha release of AdapterRemoval v3. This is a major revision\r\nof AdapterRemoval, with the goals of simplify usage by picking a sensible set of\r\ndefault settings, adding new features to handle a wider range of data, providing\r\nhuman/machine readable reports, and improving overall throughput.\r\n\r\nThis release features a number of breaking changes compared to AdapterRemoval v2\r\nand it is therefore recommended that you carefully read the list of changes\r\nbelow. Changes that affect how AdapterRemoval is used (e.g. by removing options)\r\nor that result in different output compared to AdapterRemoval v2 are marked with\r\nthe label \"[**BREAKING**]\".\r\n\r\nThis is an alpha release; not all planned features are complete (more QC reports\r\nare planned among other things), additional optimizations will be attempted, and\r\ndocumentation is still needs to be expanded further before the final release.\r\nFeedback is very welcome in the mean time.\r\n\r\nDraft documentation is available [here](https://adapterremoval.readthedocs.io/en/v3.0.0-alpha1/) and a pre-compiled binary for x86-64 Linux systems is attached below.\r\n\r\n### Added\r\n\r\n- Reports are now available in JSON format for easy parsing and in HTML format\r\n  for human consumption. These replace the old `--settings` file.\r\n- AVX2 enabled alignment algorithm for a significant performance boost (YMMV).\r\n- Added support for detecting supported CPU extensions (SSE/AVX) at runtime.\r\n- Support for combining output by simply by specifying the same filename for for\r\n  multiple outputs types, e.g. `--output1 file.fq --output2 file.fq` will for\r\n  example produce interleaved output.\r\n- Added handling for `/dev/null` as a \"magic\" output filename. Read-types\r\n  writing to this exact path will be discarded early in the pipeline, saving\r\n  time previously spent processing, compressing, and writing FASTQ reads.\r\n- Added read complexity filter inspired by [fastp].\r\n- Added the ability to only processes the first `N` reads/read pairs via the\r\n  newly added `--head N` command-line option.\r\n- Added estimation of duplication rates based on the [FastQC] algorithm.\r\n- Automatic detection of mate separators based on the first chunk of reads\r\n  processed. The `--mate-separator` is therefore only required in cases where\r\n  the results are ambiguous.\r\n- Automatic gzip compression of output files with a `.gz` extension. This makes\r\n  it possible to compress only a subset of files and removes the need for the\r\n  `--gzip` option when manually specifying output files.\r\n- Added options `--prefix-read1`, `--prefix-read2`, and `--prefix-merged` for\r\n  adding custom prefixes to the names of FASTQ reads.\r\n\r\n### Changed\r\n\r\n- [**BREAKING**] Default adapters have been changed to the [recommended Illumina\r\n  sequences], equivalent to the first 33 bp of the adapter sequences used by\r\n  AdapterRemoval v2. This makes the default settings more generally applicable.\r\n- [**BREAKING**] The trimming options `--trimwindows`, `--trimns`,\r\n  `--trimqualities`, and `--minquality` have been deprecated in favor of a new\r\n  the modified Mott's algorithm, which is enabled by default. The trimming\r\n  algorithm used may be changed using new `--trim-strategy` option.\r\n- [**BREAKING**] Merging now defaults to using the conservative algorithm,\r\n  meaning that matching quality scores are assigned `Q_match = max(Q_a, Q_b)`\r\n  instead of `Q_match ~= Q_a + Q_b`, and that same-quality mismatches are\r\n  assigned 'N' instead of one being picked at random. Motivated in part by\r\n  `doi:10.1186/s12859-018-2579-2`. This can be changed using `--merge-strategy`.\r\n- The `--merge` option no longer has any effect when processing SE data;\r\n  previously this option would treat reads with at `--minalignmentlength`\r\n  adapter as pseudo-merged reads.\r\n- [**BREAKING**] Merged reads are no longer given a `M_` name prefix and merged\r\n  reads that have been trimmed after merging are no longer given an `MT_` name\r\n  prefix. Instead, see the new option `--prefix-merged`.\r\n- [**BREAKING**] Default filenames have all been revised and now include proper\r\n  extensions to indicate the format.\r\n- [**BREAKING**] The executable is now named `adapterremoval3`. This was done to\r\n  allow v3 to coexist with AdapterRemoval v2 and to prevent accidental use of\r\n  the wrong version.\r\n- [**BREAKING**] Changed the default --maxns value from 1000 to \"infinite\"\r\n- `--gzip` now defaults to compressing independent blocks of 64kb data using\r\n  `libdeflate`. This significantly improves throughput in both single- and\r\n  (especially) multi-threaded mode, but may be incompatible with a few programs.\r\n  Compression levels of 3 and below use isa-l for compression and provides a\r\n  more universally compatible output.\r\n- The term \"merging\" is now used consistently instead of \"collapsing\", including\r\n  for default output filenames. Options have been renamed, but old option names\r\n  continue to work (except for `--outputcollapsedtruncated`).\r\n- Improvements to alignment algorithm in order to terminate early if possible.\r\n- Logging is now done more consistently and exposes options to increase or\r\n  decrease the amount of messages printed (debug, info, warning, errors).\r\n\r\n### Removed\r\n\r\nThe following changes are all [**BREAKING**] as described above:\r\n\r\n- The `--outputcollapsedtruncated` has been removed and all merged reads\r\n  (whether quality trimmed or not) are simply written to `--outputmerged`.\r\n- The `--qualitybase-output` has been removed. Output is now always Phred+33.\r\n- The `--combined-output` option has been removed in favor of allowing arbitrary\r\n  merging of output files (see above).\r\n- The `--settings` option has been replaced by `--out-json` and `--out-html` for\r\n  machine and human readable reports, respectively.\r\n- Removed support for guessing the intended command-line argument based on\r\n  prefixes. I.e. `--th` will no longer be accepted for `--threads`. Due to the\r\n  number of options added, removed, and renamed, this is no longer reliable.\r\n- The deprecated `--pcr1` and `--pcr2` options have been removed.\r\n- Dropped undocumented support for '.' as equivalent to 'N' in FASTQ reads.\r\n- Support for reading and writing of bzip2 files has been removed.\r\n","reactions":{"url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/82306102/reactions","total_count":3,"+1":0,"-1":0,"laugh":0,"hooray":3,"confused":0,"heart":0,"rocket":0,"eyes":0}},{"url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/64524252","assets_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/64524252/assets","upload_url":"https://uploads.github.com/repos/MikkelSchubert/adapterremoval/releases/64524252/assets{?name,label}","html_url":"https://github.com/MikkelSchubert/adapterremoval/releases/tag/v2.3.3","id":64524252,"author":{"login":"MikkelSchubert","id":2411627,"node_id":"MDQ6VXNlcjI0MTE2Mjc=","avatar_url":"https://avatars.githubusercontent.com/u/2411627?v=4","gravatar_id":"","url":"https://api.github.com/users/MikkelSchubert","html_url":"https://github.com/MikkelSchubert","followers_url":"https://api.github.com/users/MikkelSchubert/followers","following_url":"https://api.github.com/users/MikkelSchubert/following{/other_user}","gists_url":"https://api.github.com/users/MikkelSchubert/gists{/gist_id}","starred_url":"https://api.github.com/users/MikkelSchubert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MikkelSchubert/subscriptions","organizations_url":"https://api.github.com/users/MikkelSchubert/orgs","repos_url":"https://api.github.com/users/MikkelSchubert/repos","events_url":"https://api.github.com/users/MikkelSchubert/events{/privacy}","received_events_url":"https://api.github.com/users/MikkelSchubert/received_events","type":"User","user_view_type":"public","site_admin":false},"node_id":"RE_kwDOAS6r184D2I_c","tag_name":"v2.3.3","target_commitish":"master","name":"AdapterRemoval v2.3.3","draft":false,"immutable":false,"prerelease":false,"created_at":"2022-04-15T09:13:08Z","updated_at":"2022-04-15T09:33:40Z","published_at":"2022-04-15T09:33:40Z","assets":[],"tarball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/tarball/v2.3.3","zipball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/zipball/v2.3.3","body":"  * Updated Catch2 to fix compilation with glibc 2.34, courtesy of loganrosen. \r\n"},{"url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/39934779","assets_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/39934779/assets","upload_url":"https://uploads.github.com/repos/MikkelSchubert/adapterremoval/releases/39934779/assets{?name,label}","html_url":"https://github.com/MikkelSchubert/adapterremoval/releases/tag/v2.3.2","id":39934779,"author":{"login":"MikkelSchubert","id":2411627,"node_id":"MDQ6VXNlcjI0MTE2Mjc=","avatar_url":"https://avatars.githubusercontent.com/u/2411627?v=4","gravatar_id":"","url":"https://api.github.com/users/MikkelSchubert","html_url":"https://github.com/MikkelSchubert","followers_url":"https://api.github.com/users/MikkelSchubert/followers","following_url":"https://api.github.com/users/MikkelSchubert/following{/other_user}","gists_url":"https://api.github.com/users/MikkelSchubert/gists{/gist_id}","starred_url":"https://api.github.com/users/MikkelSchubert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MikkelSchubert/subscriptions","organizations_url":"https://api.github.com/users/MikkelSchubert/orgs","repos_url":"https://api.github.com/users/MikkelSchubert/repos","events_url":"https://api.github.com/users/MikkelSchubert/events{/privacy}","received_events_url":"https://api.github.com/users/MikkelSchubert/received_events","type":"User","user_view_type":"public","site_admin":false},"node_id":"MDc6UmVsZWFzZTM5OTM0Nzc5","tag_name":"v2.3.2","target_commitish":"master","name":"AdapterRemoval v2.3.2","draft":false,"immutable":false,"prerelease":false,"created_at":"2021-03-17T11:03:28Z","updated_at":"2021-03-17T11:26:22Z","published_at":"2021-03-17T11:26:22Z","assets":[],"tarball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/tarball/v2.3.2","zipball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/zipball/v2.3.2","body":" * Improved error messages when AdapterRemoval failed to open or write FASTQ\r\n   files (issue #42).\r\n * Fixed build on some architectures. Patch courtesy of Andreas Tille/the Debian\r\n   build team.\r\n * Fixed display of max Phred scores in FASTQ validation error messages.\r\n * Removed benchmarking scripts which were included in the repo for the sake of\r\n   making Schubert et al. 2016 reproducible. This is no longer relevant.\r\n * Use 'install' in the Makefile; patch courtesy of Eric DEVEAUD.\r\n * Added --collapse-deterministic to .settings file.\r\n * Fixed --minadapteroverlap being misapplied in PE mode.\r\n * Added --collapse-conservatively merge algorithm based on FASTQ-join. See\r\n   the man-page for more information"},{"url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/18166526","assets_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/18166526/assets","upload_url":"https://uploads.github.com/repos/MikkelSchubert/adapterremoval/releases/18166526/assets{?name,label}","html_url":"https://github.com/MikkelSchubert/adapterremoval/releases/tag/v2.3.1","id":18166526,"author":{"login":"MikkelSchubert","id":2411627,"node_id":"MDQ6VXNlcjI0MTE2Mjc=","avatar_url":"https://avatars.githubusercontent.com/u/2411627?v=4","gravatar_id":"","url":"https://api.github.com/users/MikkelSchubert","html_url":"https://github.com/MikkelSchubert","followers_url":"https://api.github.com/users/MikkelSchubert/followers","following_url":"https://api.github.com/users/MikkelSchubert/following{/other_user}","gists_url":"https://api.github.com/users/MikkelSchubert/gists{/gist_id}","starred_url":"https://api.github.com/users/MikkelSchubert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MikkelSchubert/subscriptions","organizations_url":"https://api.github.com/users/MikkelSchubert/orgs","repos_url":"https://api.github.com/users/MikkelSchubert/repos","events_url":"https://api.github.com/users/MikkelSchubert/events{/privacy}","received_events_url":"https://api.github.com/users/MikkelSchubert/received_events","type":"User","user_view_type":"public","site_admin":false},"node_id":"MDc6UmVsZWFzZTE4MTY2NTI2","tag_name":"v2.3.1","target_commitish":"master","name":"AdapterRemoval v2.3.1","draft":false,"immutable":false,"prerelease":false,"created_at":"2019-10-12T20:03:47Z","updated_at":"2019-10-12T20:08:41Z","published_at":"2019-10-12T20:08:41Z","assets":[],"tarball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/tarball/v2.3.1","zipball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/zipball/v2.3.1","body":" * Added --preserve5p option. This option prevents AdapterRemoval from trimming\r\n   the 5p of reads when the --trimqualities, --trimns, and --trimwindows options\r\n   are used. Neither end of collapsed reads are trimmed when this option is used.\r\n * Fixed Ns being miscounted as As when constructing consensus adapter sequences\r\n   using --identify-adapters."},{"url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/16066632","assets_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/16066632/assets","upload_url":"https://uploads.github.com/repos/MikkelSchubert/adapterremoval/releases/16066632/assets{?name,label}","html_url":"https://github.com/MikkelSchubert/adapterremoval/releases/tag/v2.3.0","id":16066632,"author":{"login":"MikkelSchubert","id":2411627,"node_id":"MDQ6VXNlcjI0MTE2Mjc=","avatar_url":"https://avatars.githubusercontent.com/u/2411627?v=4","gravatar_id":"","url":"https://api.github.com/users/MikkelSchubert","html_url":"https://github.com/MikkelSchubert","followers_url":"https://api.github.com/users/MikkelSchubert/followers","following_url":"https://api.github.com/users/MikkelSchubert/following{/other_user}","gists_url":"https://api.github.com/users/MikkelSchubert/gists{/gist_id}","starred_url":"https://api.github.com/users/MikkelSchubert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MikkelSchubert/subscriptions","organizations_url":"https://api.github.com/users/MikkelSchubert/orgs","repos_url":"https://api.github.com/users/MikkelSchubert/repos","events_url":"https://api.github.com/users/MikkelSchubert/events{/privacy}","received_events_url":"https://api.github.com/users/MikkelSchubert/received_events","type":"User","user_view_type":"public","site_admin":false},"node_id":"MDc6UmVsZWFzZTE2MDY2NjMy","tag_name":"v2.3.0","target_commitish":"master","name":"AdapterRemoval v2.3.0","draft":false,"immutable":false,"prerelease":false,"created_at":"2019-03-12T16:37:23Z","updated_at":"2019-03-12T17:06:59Z","published_at":"2019-03-12T17:06:59Z","assets":[],"tarball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/tarball/v2.3.0","zipball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/zipball/v2.3.0","body":" * Fixed --collapse producing slightly different result on 32 bit and 64 bit\r\n   architectures. Courtesy of Andreas Tille.\r\n * Added support for output files without a basename; to create such output\r\n   files, use an empty basename (--basename \"\") or a basename ending with a \r\n   slash (--basename path/).\r\n * Added support for managing file handles to allow AdapterRemoval to run\r\n   when the the number of output files exceeds the number of file handles, e.g.\r\n   when demultiplexing large numbers of samples.\r\n * Reworked demultiplexing to improve performance for many paired barcodes."},{"url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/15471037","assets_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/15471037/assets","upload_url":"https://uploads.github.com/repos/MikkelSchubert/adapterremoval/releases/15471037/assets{?name,label}","html_url":"https://github.com/MikkelSchubert/adapterremoval/releases/tag/v2.2.4","id":15471037,"author":{"login":"MikkelSchubert","id":2411627,"node_id":"MDQ6VXNlcjI0MTE2Mjc=","avatar_url":"https://avatars.githubusercontent.com/u/2411627?v=4","gravatar_id":"","url":"https://api.github.com/users/MikkelSchubert","html_url":"https://github.com/MikkelSchubert","followers_url":"https://api.github.com/users/MikkelSchubert/followers","following_url":"https://api.github.com/users/MikkelSchubert/following{/other_user}","gists_url":"https://api.github.com/users/MikkelSchubert/gists{/gist_id}","starred_url":"https://api.github.com/users/MikkelSchubert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MikkelSchubert/subscriptions","organizations_url":"https://api.github.com/users/MikkelSchubert/orgs","repos_url":"https://api.github.com/users/MikkelSchubert/repos","events_url":"https://api.github.com/users/MikkelSchubert/events{/privacy}","received_events_url":"https://api.github.com/users/MikkelSchubert/received_events","type":"User","user_view_type":"public","site_admin":false},"node_id":"MDc6UmVsZWFzZTE1NDcxMDM3","tag_name":"v2.2.4","target_commitish":"master","name":"AdapterRemoval v2.2.4","draft":false,"immutable":false,"prerelease":false,"created_at":"2019-02-10T16:44:28Z","updated_at":"2019-02-10T16:56:18Z","published_at":"2019-02-10T16:56:18Z","assets":[],"tarball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/tarball/v2.2.4","zipball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/zipball/v2.2.4","body":"  * Fixed bug in --trim5p N which would AdapterRemoval to abort if N was greater\r\n    than the pre-trimmed read length.\r\n  * Fixed --identify-adapters not respecting the --mate-separator option.\r\n"},{"url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/15121550","assets_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/15121550/assets","upload_url":"https://uploads.github.com/repos/MikkelSchubert/adapterremoval/releases/15121550/assets{?name,label}","html_url":"https://github.com/MikkelSchubert/adapterremoval/releases/tag/v2.2.3","id":15121550,"author":{"login":"MikkelSchubert","id":2411627,"node_id":"MDQ6VXNlcjI0MTE2Mjc=","avatar_url":"https://avatars.githubusercontent.com/u/2411627?v=4","gravatar_id":"","url":"https://api.github.com/users/MikkelSchubert","html_url":"https://github.com/MikkelSchubert","followers_url":"https://api.github.com/users/MikkelSchubert/followers","following_url":"https://api.github.com/users/MikkelSchubert/following{/other_user}","gists_url":"https://api.github.com/users/MikkelSchubert/gists{/gist_id}","starred_url":"https://api.github.com/users/MikkelSchubert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MikkelSchubert/subscriptions","organizations_url":"https://api.github.com/users/MikkelSchubert/orgs","repos_url":"https://api.github.com/users/MikkelSchubert/repos","events_url":"https://api.github.com/users/MikkelSchubert/events{/privacy}","received_events_url":"https://api.github.com/users/MikkelSchubert/received_events","type":"User","user_view_type":"public","site_admin":false},"node_id":"MDc6UmVsZWFzZTE1MTIxNTUw","tag_name":"v2.2.3","target_commitish":"master","name":"AdapterRemoval v2.2.3","draft":false,"immutable":false,"prerelease":false,"created_at":"2019-01-22T21:39:48Z","updated_at":"2019-01-22T21:41:20Z","published_at":"2019-01-22T21:41:20Z","assets":[],"tarball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/tarball/v2.2.3","zipball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/zipball/v2.2.3","body":"  * Added support for trimming reads by a fixed amount: --trim5p N --trim3p N.\r\n    Different values may be given for each mate: --trim5p N1 N2. Trimming is\r\n    carried out after adapters have been removed and reads have been collapsed,\r\n    if enabled, but before quality trimming (Ns and low qualities).\r\n  * Added option for determistic read merging (--collapse-deterministic). In\r\n    this mode AdapterRemoval will set a merged base to 'N' with quality 0 if\r\n    the corresponding bases on the two mates differ, and if both have the same\r\n    quality score. The default behavior is to select one of the two bases at\r\n    random.\r\n  * Fixed reporting of line numbers in error messages.\r\n  * Added conda installation instructions, courtesy of Maxime Borry (maxibor).\r\n  * Fixed reading mate 2 adapters specified via --adapter-list. Adapters would\r\n    be used in the reverse orientation compared to --adapter2. Courtesy of\r\n    Karolis (KarolisM).\r\n  * Fixed various typos and improved help/error 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This is\r\n    supported for all operations. Special thanks to Stephen Clayton.\r\n  * Added additional run-time checks to catch race-conditions.\r\n  * Progress messages written to STDERR no longer cause subsequent error\r\n    messages to be written to the same line.\r\n  * Implemented quality trimming using a sliding window approach inspired by\r\n    sickle (https://github.com/najoshi/sickle). Special thanks to Kevin Murray.\r\n  * Fixed miscounting of the total number of retained nucleotides, where mate 1\r\n    reads were being counted twice instead of counting both mate 1 and mate 2.\r\n"},{"url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/4499733","assets_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/4499733/assets","upload_url":"https://uploads.github.com/repos/MikkelSchubert/adapterremoval/releases/4499733/assets{?name,label}","html_url":"https://github.com/MikkelSchubert/adapterremoval/releases/tag/v2.2.0","id":4499733,"author":{"login":"MikkelSchubert","id":2411627,"node_id":"MDQ6VXNlcjI0MTE2Mjc=","avatar_url":"https://avatars.githubusercontent.com/u/2411627?v=4","gravatar_id":"","url":"https://api.github.com/users/MikkelSchubert","html_url":"https://github.com/MikkelSchubert","followers_url":"https://api.github.com/users/MikkelSchubert/followers","following_url":"https://api.github.com/users/MikkelSchubert/following{/other_user}","gists_url":"https://api.github.com/users/MikkelSchubert/gists{/gist_id}","starred_url":"https://api.github.com/users/MikkelSchubert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MikkelSchubert/subscriptions","organizations_url":"https://api.github.com/users/MikkelSchubert/orgs","repos_url":"https://api.github.com/users/MikkelSchubert/repos","events_url":"https://api.github.com/users/MikkelSchubert/events{/privacy}","received_events_url":"https://api.github.com/users/MikkelSchubert/received_events","type":"User","user_view_type":"public","site_admin":false},"node_id":"MDc6UmVsZWFzZTQ0OTk3MzM=","tag_name":"v2.2.0","target_commitish":"main","name":"AdapterRemoval v2.2.0","draft":false,"immutable":false,"prerelease":false,"created_at":"2016-10-27T12:44:15Z","updated_at":"2016-10-27T12:49:49Z","published_at":"2016-10-27T12:49:49Z","assets":[],"tarball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/tarball/v2.2.0","zipball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/zipball/v2.2.0","body":"- AdapterRemoval now requires a C++11 compliant compiler; furthermore,\n  multithreading is no longer an optional feature, as this is now\n  implemented using the C++11 instead of directly calling pthreads.\n- Add explicit message not to use the results after failed runs.\n- Minor changes to .settings: Adapter numbers now 1-based; the 'Number of\n  reads with adapters' is changed to 'Number of read pairs with adapters'\n  when trimming PE reads; the 'Average read length of trimmed reads' is\n  changed to 'Average read length of retained reads' for clarity.\n- Dropped the undocumented 'poor' classification for alignments; for\n  statistical purposes, reads are either counted as aligned or not aligned.\n  This ony changes how results are presented in the .settings files.\n- Rework selection of nucleotides at overlapping positions with the same\n  quality, in order to prevent potential data-races during tie-breaking,\n  when running in multi-threaded mode.\n- Added support for reading FASTQ files using Windows-style newlines (\\r\\n).\n- AdapterRemoval will not print a warning to STDERR if the same command-line\n  option is specified multiple times.\n- Reworked handling of barcodes to avoid unnecessary memory allocations,\n  which would cause problems when using long barcodes.\n- Added support for combining output files; this is enabled using the\n  --combined-output option, and ensures that all reads are written to the\n  same file, or pair of files (for non-interleaved PE reads). The sequence\n  of reads that fail are replaced with a single 'N' with quality score 0.\n- Fixed bug in the counting of singleton reads used in '.settings' files.\n- Fixed mis-placement of underscore when pretty printing adapter sequences\n  that included barcodes.\n- Fixed misprinting of mate 2 adapter sequences in the .settings file;\n  these would be printed in the reverse complemented orientation, relative\n  to how they were specified on the command-line.\n"},{"url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/2793522","assets_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/releases/2793522/assets","upload_url":"https://uploads.github.com/repos/MikkelSchubert/adapterremoval/releases/2793522/assets{?name,label}","html_url":"https://github.com/MikkelSchubert/adapterremoval/releases/tag/v2.1.7","id":2793522,"author":{"login":"MikkelSchubert","id":2411627,"node_id":"MDQ6VXNlcjI0MTE2Mjc=","avatar_url":"https://avatars.githubusercontent.com/u/2411627?v=4","gravatar_id":"","url":"https://api.github.com/users/MikkelSchubert","html_url":"https://github.com/MikkelSchubert","followers_url":"https://api.github.com/users/MikkelSchubert/followers","following_url":"https://api.github.com/users/MikkelSchubert/following{/other_user}","gists_url":"https://api.github.com/users/MikkelSchubert/gists{/gist_id}","starred_url":"https://api.github.com/users/MikkelSchubert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MikkelSchubert/subscriptions","organizations_url":"https://api.github.com/users/MikkelSchubert/orgs","repos_url":"https://api.github.com/users/MikkelSchubert/repos","events_url":"https://api.github.com/users/MikkelSchubert/events{/privacy}","received_events_url":"https://api.github.com/users/MikkelSchubert/received_events","type":"User","user_view_type":"public","site_admin":false},"node_id":"MDc6UmVsZWFzZTI3OTM1MjI=","tag_name":"v2.1.7","target_commitish":"master","name":"AdapterRemoval v2.1.7","draft":false,"immutable":false,"prerelease":false,"created_at":"2016-03-12T11:21:27Z","updated_at":"2016-03-12T11:21:47Z","published_at":"2016-03-12T11:21:47Z","assets":[],"tarball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/tarball/v2.1.7","zipball_url":"https://api.github.com/repos/MikkelSchubert/adapterremoval/zipball/v2.1.7","body":"- The mate number is now stripped from collapsed reads, where previously this\n  would always be '\\1' (if set). However, if meta-data is present in the\n  reads, that found in the mate 1 read is retained.\n- The value used for --mate-separator is now written to the 'settings' file.\n- Improved 'make install'. This command now makes use of a PREFIX value to\n  determine the installation destination (defaults to /usr/local), and\n  includes the 'README.md' file and 'examples' folder in the installation.\n- Improved 'make test'. This command now attempts to download the required\n  testing library automatically, using either wget or curl if available.\n"}]