CHANGES.rst

Changelog

v4.9 (2024-06-19)

• Added --action=crop for removing everything except the adapter sequence. (The sequence before and after the adapter is removed.) This can be useful if the "adapter" contains wildcards (such as N) that you are interested in.
• :issue:`788`: Added option -L as a counterpart to -l/--length, which allows shortening R1 and R2 to different lengths.
• A too long minimum overlap is now automatically decreased to the length of the adapter. That is, you can use -a 'ACGT;o=99' to force full-length matches.
• :issue:`784`: Fixed some unexpected trimming results for anchored 5' adapters (due to an incorrectly initialized alignment score matrix).

v4.8 (2024-04-12)

• :issue:`772`: Restored ability to provide input files via process substitution.
• :issue:`773`: Fixed crash when writing interleaved data to stdout (that is, when no -o option is provided).

v4.7 (2024-03-14)

• :issue:`767`: Error messages are always sent to stderr. They were previously sent to stdout when using -o.
• Cutadapt can now read single-end data from unaligned BAM files (uBAM).
• Dropped support for Python 3.7.

v4.6 (2023-12-06)

• :issue:`744`, :issue:`561`: Make --revcomp work with paired-end data.

v4.5 (2023-10-06)

• :pr:`725`: Added a --max-average-error-rate/--max-aer option to add a filter that checks if the number of expected errors divided by read length is above a certain threshold. The expected errors are calculated the same as in --max-expected-errors, and dividing by read length helps for reads that have varying lengths.
• :issue:`696`: Added a histogram of the lengths of removed poly-A tails to the report.
• :issue:`696`: For paired-end data, --poly-a was changed to trim poly-T "heads" on R2 (this is still experimental as it is unclear whether that is the desired behavior. Please give feedback!)
• A poly-A tail is only removed if it is at least three nucleotides long.
• :issue:`734`: Fixed misassignments during demultiplexing that would sometimes happen when there are collisions between adapter sequences (when the warning "sequence ... cannot be assigned uniquely" was printed). Previously, sequences could incorrectly be assigned to an adapter that is not actually the best match.

v4.4 (2023-04-28)

• :issue:`695`: Fixed very slow k-mer heuristic initialization (hours instead of seconds) for degenerate adapter sequences such as A{100} as used when doing poly-A trimming.
• :issue:`696`: Added option --poly-a for trimming poly-A tails. This is more accurate and multiple times faster than using -a A{100} as previously recommended. This is currently experimental (that is, the algorithm may change in the next one or two releases).
• :issue:`685`: Sped up index generation somewhat. This is most noticable when demultiplexing using thousands or more adapters. The speedup is different depending on whether indels are allowed or not because different algorithms are used.
• :issue:`685`: Sped up demultiplexing (when using an index) for the case when the read contains N bases within the region where the adapter matches. Previously, any N would disable the index for that read and trigger a fallback to the slow method of matching each adapter one-by-one. Now the index is used even in those cases.
• :pr:`700`: Sped up --max-expected-errors. Thanks @rhpvorderman.

v4.3 (2023-03-17)

• :pr:`663`: Cutadapt became significantly faster due to an added runtime heuristic that avoids running the full alignment algorithm if it can be proven that it cannot succeed. Thanks to @rhpvorderman for this great improvement!
• :issue:`665`: 5' adapters did not allow partial matches in the beginning when the :ref:`rightmost <rightmost>` adapter-search parameter was used.
• :issue:`662`: Fixed assertion error when --discard-untrimmed was used together with --json and demultiplexing.
• :issue:`674`: When reading 3' adapters from an external file, they can now all be anchored by using the syntax -a file$:adapters.fasta (note the $ in file$:).
• :issue:`669`: The --rename option now understands the \t escape sequence and will insert a tab character in its place. This is useful when transferring FASTQ header comments to SAM tags.

v4.2 (2022-12-09)

• :issue:`654`: When determining the error rate for a partial match of an adapter with N wildcards, the number of non-N bases was not computed correctly, which could lead to matches not being found.
• :issue:`546`: Automatically replace I in adapter sequences with N. I is used to encode inosine, which matches any base. Contributed by @peterjc.
• :issue:`528`: Cutadapt should now no long hang in multicore mode when an error was raised in a worker process (for example, when an incorrectly formatted FASTQ file was encountered).

v4.1 (2022-06-07)

• :issue:`624`: You can now combine reading adapter sequences from an external file with the search parameter notation. For example, -a "file:adapters.fasta;min_overlap=5" sets the minimum overlap to 5 for all adapters in adapters.fasta.
• :issue:`361`: When reading 5' adapters from an external file, they can now all be anchored by using the syntax -g ^file:adapters.fasta (note the ^ before file:).
• :issue:`254`: Finding the rightmost 5' adapter occurrence is now supported by using the rightmost search parameter (the default is to find the leftmost occurrence).
• :issue:`615`: Fix linked adapter statistics for 5' and 3' end not being reported separated correctly.
• :issue:`616`: Report correct number of quality-trimmed bases when both -q and --nextseq-trim are used.

v4.0 (2022-04-13)

• :issue:`604`, :pr:`608`: The :ref:`alignment algorithm was tweaked <algorithm-indel-scores>` to penalize indels more and to more accurately pick the leftmost adapter occurrence if there are multiple. This will normally affect very few reads, but should generally lead to fewer surprising results in cases where it matters. Because this changes trimming results, it was appropriate to bump the major version to 4.
• :issue:`607`: Print an error when an output file was specified multiple times (for example, for --untrimmed-output and --too-short-output). Sending output from different filters to the same file is not supported at the moment.
• :issue:`603`: When -e was used with an absolute number of errors and there were N wildcards in the sequence, the actual number of allowed errors was too low.
• Speed up quality trimming (both -q and --nextseq-trim) somewhat.
• Python 3.6 is no longer supported as it is end-of-life.

v3.7 (2022-02-23)

• :issue:`600`: Fixed {match_sequence} placeholder not working when renaming paired-end reads.

v3.6 (2022-02-18)

• :issue:`437`: Add {match_sequence} to the placeholders that --rename accepts. This allows to add the sequence matching an adapter (including errors) to the read header. An empty string is inserted if there is no match.
• :issue:`589`: Windows wheels are now available on PyPI. That is, pip install will no longer attempt to compile things, but just install a pre-compiled binary.
• :issue:`592`: Clarify in documentation and error messages that anchored adapters need to match in full and that therefore setting an explict minimum overlap (min_overlap=, o=) for them is not possible.

v3.5 (2021-09-29)

• :issue:`555`: Add support for dumping statistics in JSON format using --json.
• :issue:`541`: Add a "Read fate breakdown" section heading to the report, and also add statistics for reads discarded because of --discard-untrimmed and --discard-trimmed. With this, the numbers in that section should add up to 100%.
• Add option -Q, which allows to specify a quality-trimming threshold for R2 that is different from the one for R1.
• :issue:`567`: Add noindels adapter-trimming parameter. You can now write -a "ADAPTER;noindels" to disallow indels for a single adapter only.
• :issue:`570`: Fix --pair-adapters not finding some pairs when reads contain more than one adapter.
• :issue:`524`: Fix a memory leak when using --info-file with multiple cores.
• :issue:`559`: Fix adjacent base statistics not being shown for linked adapters.

v3.4 (2021-03-30)

• :issue:`481`: An experimental single-file Windows executable of Cutadapt is available for download on the GitHub "releases" page.
• :issue:`517`: Report correct sequence in info file if read was reverse complemented
• :issue:`517`: Added a column to the info file that shows whether the read was reverse-complemented (if --revcomp was used)
• :issue:`320`: Fix (again) "Too many open files" when demultiplexing

v3.3 (2021-03-04)

• :issue:`504`: Fix a crash on Windows.
• :issue:`490`: When --rename is used with --revcomp, disable adding the rc suffix to reads that were reverse-complemented.
• Also, there is now a {rc} template variable for the --rename option, which is replaced with "rc" if the read was reverse-complemented (and the empty string if not).
• :issue:`512`: Fix issue :issue:`128` once more (the “Reads written” figure in the report incorrectly included both trimmed and untrimmed reads if --untrimmed-output was used).
• :issue:`515`: The report is now sent to stderr if any output file is written to stdout

v3.2 (2021-01-07)

• :issue:`437`: Implement a --rename option for :ref:`flexible read name modifications <read-renaming>` such as moving a barcode sequence into the read name.
• :issue:`503`: The index for demultiplexing is now created a lot faster (within seconds instead of minutes) when allowing indels.
• :issue:`499`: Fix combinatorial demultiplexing not working when using multiple cores.

v3.1 (2020-12-03)

• :issue:`443`: With --action=retain, it is now possible to trim reads while leaving the adapter sequence itself in the read. That is, only the sequence before (for 5’ adapters) or after (for 3’ adapters) is removed. With linked adapters, both adapters are retained.
• :issue:`495`: Running with multiple cores did not work using macOS and Python 3.8+. To prevent problems like these in the future, automated testing has been extended to also run on macOS.
• :issue:`482`: Print statistics for --discard-casava and --max-ee in the report.
• :issue:`497`: The changelog for 3.0 previously forgot to mention that the following options, which were deprecated in version 2.0, have now been removed, and using them will lead to an error: --format, --colorspace, -c, -d, --double-encode, -t, --trim-primer, --strip-f3, --maq, --bwa, --no-zero-cap. This frees up some single-character options, allowing them to be re-purposed for future Cutadapt features.

v3.0 (2020-11-10)

• Demultiplexing on multiple cores is now supported. This was the last feature that only ran single-threaded.
• :issue:`478`: Demultiplexing now always generates all possible output files.
• :issue:`358`: You can now use -e also :ref:`to specify the maximum number of errors <error-tolerance>` (instead of the maximum error rate). For example, write -e 2 to allow two errors over a full-length adapter match.
• :pr:`486`: Trimming many anchored adapters (for example when demultiplexing) is now faster by using an index even when indels are allowed. Previously, Cutadapt would only be able to build an index with --no-indels.
• :issue:`469`: Cutadapt did not run under Python 3.8 on recent macOS versions.
• :issue:`425`: Change the default compression level for .gz output files from 6 to 5. This reduces the time used for compression by about 50% while increasing file size by less than 10%. To get the old behavior, use --compression-level=6. If you use Cutadapt to create intermediate files that are deleted anyway, consider also using the even faster option -Z (same as --compression-level=1).
• :pr:`485`: Fix that, under some circumstances, in particular when trimming a 5' adapter and there was a mismatch in its last nucleotide(s), not the entire adapter sequence would be trimmed from the read. Since fixing this required changed the alignment algorithm slightly, this is a backwards incompatible change.
• Fix that the report did not include the number of reads that are too long, too short or had too many N. (This unintentionally disappeared in a previous version.)
• :issue:`487`: When demultiplexing, the reported number of written pairs was always zero.
• :issue:`497`: The following options, which were deprecated in version 2.0, have been removed, and using them will lead to an error: --format, --colorspace, -c, -d, --double-encode, -t, --trim-primer, --strip-f3, --maq, --bwa, --no-zero-cap. This frees up some single-character options, allowing them to be re-purposed for future Cutadapt features.
• Ensure Cutadapt runs under Python 3.9.
• Drop support for Python 3.5.

v2.10 (2020-04-22)

• Fixed a performance regression introduced in version 2.9.
• :pr:`449`: --action= could not be used with --pair-adapters. Fix contributed by wlokhorst.
• :issue:`450`: --untrimmed-output, --too-short-output and --too-long-output can now be written interleaved.
• :issue:`453`: Fix problem that N wildcards in adapters did not match N characters in the read. N characters now match any character in the read, independent of whether --match-read-wildcards is used or not.
• With --action=lowercase/mask, print which sequences would have been removed in the “Overview of removed sequences” statistics. Previously, it would show that no sequences have been removed.

v2.9 (2020-03-18)

• :issue:`441`: Add a --max-ee (or --max-expected-errors) option for filtering reads whose number of expected errors exceeds the given threshold. The idea comes from Edgar et al. (2015).
• :issue:`438`: The info file now contains the rc suffix that is added to the names of reverse-complemented reads (with --revcomp).
• :issue:`448`: .bz2 and .xz output wasn’t possible in multi-core mode.

v2.8 (2020-01-13)

• :issue:`220`: With option --revcomp, Cutadapt now searches both the read and its reverse complement for adapters. The version that matches best is kept. This can be used to “normalize” strandedness.
• :issue:`430`: --action=lowercase now works with linked adapters
• :issue:`431`: Info files can now be written even for linked adapters.

v2.7 (2019-11-22)

• :issue:`427`: Multicore is now supported even when using --info-file, --rest-file or --wildcard-file. The only remaining feature that still does not work with multicore is now demultiplexing.
• :issue:`290`: When running on a single core, Cutadapt no longer spawns external pigz processes for writing gzip-compressed files. This is a first step towards ensuring that using --cores=n uses only at most n CPU cores.
• This release adds support for Python 3.8.

v2.6 (2019-10-26)

• :issue:`395`: Do not show animated progress when --quiet is used.
• :issue:`399`: When two adapters align to a read equally well (in terms of the number of matches), prefer the alignment that has fewer errors.
• :issue:`401` Give priority to adapters given earlier on the command line. Previously, the priority was: All 3' adapters, all 5' adapters, all anywhere adapters. In rare cases this could lead to different results.
• :issue:`404`: Fix an issue preventing Cutadapt from being used on Windows.
• This release no longer supports Python 3.4 (which has reached end of life).

v2.5 (2019-09-04)

• :issue:`391`: Multicore is now supported even when using --untrimmed-output, --too-short-output, --too-long-output or the corresponding ...-paired-output options.
• :issue:`393`: Using --info-file no longer crashes when processing paired-end data. However, the info file itself will only contain results for R1.
• :issue:`394`: Options -e/--no-indels/-O were ignored for linked adapters
• :issue:`320`: When a “Too many open files” error occurs during demultiplexing, Cutadapt can now automatically raise the limit and re-try if the limit is a “soft” limit.

v2.4 (2019-07-09)

• :issue:`292`: Implement support for demultiplexing paired-end reads that use :ref:`combinatorial indexing (“combinatorial demultiplexing”) <combinatorial-demultiplexing>`.
• :pr:`384`: Speed up reading compressed files by requiring an xopen version that uses an external pigz process even for reading compressed input files (not only for writing).
• :issue:`381`: Fix --report=minimal not working.
• :issue:`380`: Add a --fasta option for forcing that FASTA is written to standard output even when input is FASTQ. Previously, forcing FASTA was only possible by providing an output file name.

v2.3 (2019-04-25)

• :issue:`378`: The --pair-adapters option, added in version 2.1, was not actually usable for demultiplexing.

v2.2 (2019-04-20)

• :issue:`376`: Fix a crash when using anchored 5' adapters together with --no-indels and trying to trim an empty read.
• :issue:`369`: Fix a crash when attempting to trim an empty read using a -g adapter with wildcards.

v2.1 (2019-03-15)

• :issue:`366`: Fix problems when combining --cores with reading from standard input or writing to standard output.
• :issue:`347`: Support :ref:`“paired adapters” <paired-adapters>`. One use case is demultiplexing Illumina Unique Dual Indices (UDI).

v2.0 (2019-03-06)

This is a major new release with lots of bug fixes and new features, but also some backwards-incompatible changes. These should hopefully not affect too many users, but please make sure to review them and possibly update your scripts!

Backwards-incompatible changes

• :issue:`329`: Linked adapters specified with -a ADAPTER1...ADAPTER2 are no longer anchored by default. To get results consist with the old behavior, use -a ^ADAPTER1...ADAPTER2 instead.
• Support for colorspace data was removed. Thus, the following command-line options can no longer be used: -c, -d, -t, --strip-f3, --maq, --bwa, --no-zero-cap.
• “Legacy mode” has been removed. This mode was enabled under certain conditions and would change the behavior such that the read-modifying options such as -q would only apply to the forward/R1 reads. This was necessary for compatibility with old Cutadapt versions, but became increasingly confusing.
• :issue:`360`: Computation of the error rate of an adapter match no longer counts the N wildcard bases. Previously, an adapter like N{18}CC (18 N wildcards followed by CC) would effectively match anywhere because the default error rate of 0.1 (10%) would allow for two errors. The error rate of a match is now computed as the number of non-N bases in the matching part of the adapter divided by the number of errors.
• This release of Cutadapt requires at least Python 3.4 to run. Python 2.7 is no longer supported.

Features

• A progress indicator is printed while Cutadapt is working. If you redirect standard error to a file, the indicator is disabled.
• Reading of FASTQ files has gotten faster due to a new parser. The FASTA and FASTQ reading/writing functions are now available as part of the dnaio library. This is a separate Python package that can be installed independently from Cutadapt. There is one regression at the moment: FASTQ files that use a second header (after the "+") will have that header removed in the output.
• Some other performance optimizations were made. Speedups of up to 15% are possible.
• Demultiplexing has become a lot faster :ref:`under certain conditions <speed-up-demultiplexing>`.
• :issue:`335`: For linked adapters, it is now possible to :ref:`specify which of the two adapters should be required <linked-override>`, overriding the default.
• :issue:`166`: By specifying --action=lowercase, it is now possible to not trim adapters, but to instead convert the section of the read that would have been trimmed to lowercase.

Bug fixes

• Removal of legacy mode fixes also :issue:`345`: --length would not enable legacy mode.
• The switch to dnaio also fixed :issue:`275`: Input files with non-standard names now no longer lead to a crash. Instead the format is now recognized from the file content.
• Fix :issue:`354`: Sequences given using file: can now be unnamed.
• Fix :issue:`257` and :issue:`242`: When only R1 or only R2 adapters are given, the --pair-filter setting is now forced to both for the --discard-untrimmed (and --untrimmed-(paired-)output) filters. Otherwise, with the default --pair-filter=any, all pairs would be considered untrimmed because one of the reads in the pair is always untrimmed.

Other

• :issue:`359`: The -f/--format option is now ignored and a warning will be printed if it is used. The input file format is always auto-detected.

v1.18 (2018-09-07)

Features

• Close :issue:`327`: Maximum and minimum lengths can now be specified separately for R1 and R2 with -m LENGTH1:LENGTH2. One of the lengths can be omitted, in which case only the length of the other read is checked (as in -m 17: or -m :17).
• Close :issue:`322`: Use -j 0 to auto-detect how many cores to run on. This should even work correctly on cluster systems when Cutadapt runs as a batch job to which fewer cores than exist on the machine have been assigned. Note that the number of threads used by pigz cannot be controlled at the moment, see :issue:`290`.
• Close :issue:`225`: Allow setting the maximum error rate and minimum overlap length per adapter. A new :ref:`syntax for adapter-specific parameters <trimming-parameters>` was added for this. Example: -a "ADAPTER;min_overlap=5".
• Close :issue:`152`: Using the new syntax for adapter-specific parameters, it is now possible to allow partial matches of a 3' adapter at the 5' end (and partial matches of a 5' adapter at the 3' end) by specifying the anywhere parameter (as in -a "ADAPTER;anywhere").
• Allow --pair-filter=first in addition to both and any. If used, a read pair is discarded if the filtering criterion applies to R1; and R2 is ignored.
• Close :issue:`112`: Implement a --report=minimal option for printing a succinct two-line report in tab-separated value (tsv) format. Thanks to :user:`jvolkening` for coming up with an initial patch!

Bug fixes

• Fix :issue:`128`: The “Reads written” figure in the report incorrectly included both trimmed and untrimmed reads if --untrimmed-output was used.

Other

• The options --no-trim and --mask-adapter should now be written as --action=mask and --action=none. The old options still work.
• This is the last release to support colorspace data
• This is the last release to support Python 2.

v1.17 (2018-08-20)

• Close :issue:`53`: Implement adapters :ref:`that disallow internal matches <non-internal>`. This is a bit like anchoring, but less strict: The adapter sequence can appear at different lengths, but must always be at one of the ends. Use -a ADAPTERX (with a literal X) to disallow internal matches for a 3' adapter. Use -g XADAPTER to disallow for a 5' adapter.
• :user:`klugem` contributed PR :issue:`299`: The --length option (and its alias -l) can now be used with negative lengths, which will remove bases from the beginning of the read instead of from the end.
• Close :issue:`107`: Add a --discard-casava option to remove reads that did not pass CASAVA filtering (this is possibly relevant only for older datasets).
• Fix :issue:`318`: Cutadapt should now be installable with Python 3.7.
• Running Cutadapt under Python 3.3 is no longer supported (Python 2.7 or 3.4+ are needed)
• Planned change: One of the next Cutadapt versions will drop support for Python 2 entirely, requiring Python 3.

v1.16 (2018-02-21)

• Fix :issue:`291`: When processing paired-end reads with multiple cores, there could be errors about incomplete FASTQs although the files are intact.
• Fix :issue:`280`: Quality trimming statistics incorrectly show the same values for R1 and R2.

v1.15 (2017-11-23)

• Cutadapt can now run on multiple CPU cores in parallel! To enable it, use the option -j N (or the long form --cores=N), where N is the number of cores to use. Multi-core support is only available on Python 3, and not yet with some command-line arguments. See :ref:`the new section about multi-core in the documentation <multicore>` for details. When writing .gz files, make sure you have pigz installed to get the best speedup.
• The plan is to make multi-core the default (automatically using as many cores as are available) in future releases, so please test it and report an issue if you find problems!
• Issue :issue:`256`: --discard-untrimmed did not have an effect on non-anchored linked adapters.
• Issue :issue:`118`: Added support for demultiplexing of paired-end data.

v1.14 (2017-06-16)

• Fix: Statistics for 3' part of a linked adapter were reported incorrectly
• Fix issue #244: Quality trimming with --nextseq-trim would not apply to R2 when trimming paired-end reads.
• --nextseq-trim now disables legacy mode.
• Fix issue #246: installation failed on non-UTF8 locale

v1.13 (2017-03-16)

• The 3' adapter of linked adapters can now be anchored. Write -a ADAPTER1...ADAPTER2$ to enable this. Note that the 5' adapter is always anchored in this notation.
• Issue #224: If you want the 5' part of a linked adapter not to be anchored, you can now write -g ADAPTER...ADAPTER2 (note -g instead of -a). This feature is experimental and may change behavior in the next release.
• Issue #236: For more accurate statistics, it is now possible to specify the GC content of the input reads with --gc-content. This does not change trimming results, only the number in the "expect" column of the report. Since this is probably not needed by many people, the option is not listed when running cutadapt --help.
• Issue #235: Adapter sequences are now required to contain only valid IUPAC codes (lowercase is also allowed, U is an alias for T). This should help to catch hard-to-find bugs, especially in scripts. Use option -N to match characters literally (possibly useful for amino acid sequences).
• Documentation updates and some refactoring of the code

v1.12 (2016-11-28)

• Add read modification option --length (short: --l), which will shorten each read to the given length.
• Cutadapt will no longer complain that it has nothing to do when you do not give it any adapters. For example, you can use this to convert file formats: cutadapt -o output.fasta input.fastq.gz converts FASTQ to FASTA.
• The xopen module for opening compressed files was moved to a separate package on PyPI.

v1.11 (2016-08-16)

• The --interleaved option no longer requires that both input and output is interleaved. It is now possible to have two-file input and interleaved output, and to have interleaved input and two-file output.
• Fix issue #202: First and second FASTQ header could get out of sync when options modifying the read name were used.

v1.10 (2016-05-19)

• Added a new “linked adapter” type, which can be used to search for a 5' and a 3' adapter at the same time. Use -a ADAPTER1...ADAPTER2 to search for a linked adapter. ADAPTER1 is interpreted as an anchored 5' adapter, which is searched for first. Only if ADAPTER1 is found will ADAPTER2 be searched for, which is a regular 3' adapter.
• Added experimental --nextseq-trim option for quality trimming of NextSeq data. This is necessary because that machine cannot distinguish between G and reaching the end of the fragment (it encodes G as 'black').
• Even when trimming FASTQ files, output can now be FASTA (quality values are simply dropped). Use the -o/-p options with a file name that ends in .fasta or .fa to enable this.
• Cutadapt does not bundle pre-compiled C extension modules (.so files) anymore. This affects only users that run cutadapt directly from an unpacked tarball. Install through pip or conda instead.
• Fix issue #167: Option --quiet was not entirely quiet.
• Fix issue #199: Be less strict when checking for properly-paired reads.
• This is the last version of cutadapt to support Python 2.6. Future versions will require at least Python 2.7.

v1.9.1 (2015-12-02)

• Added --pair-filter option, which :ref:`modifies how filtering criteria apply to paired-end reads <filtering-paired>`
• Add --too-short-paired-output and --too-long-paired-output options.
• Fix incorrect number of trimmed bases reported if --times option was used.

v1.9 (2015-10-29)

• Indels in the alignment can now be disabled for all adapter types (use --no-indels).
• Quality values are now printed in the info file (--info-file) when trimming FASTQ files. Fixes issue #144.
• Options --prefix and --suffix, which modify read names, now accept the placeholder {name} and will replace it with the name of the found adapter. Fixes issue #104.
• Interleaved FASTQ files: With the --interleaved switch, paired-end reads will be read from and written to interleaved FASTQ files. Fixes issue #113.
• Anchored 5' adapters can now be specified by writing -a SEQUENCE... (note the three dots).
• Fix --discard-untrimmed and --discard-trimmed not working as expected in paired-end mode (issue #146).
• The minimum overlap is now automatically reduced to the adapter length if it is too large. Fixes part of issue #153.
• Thanks to Wolfgang Gerlach, there is now a Dockerfile.
• The new --debug switch makes cutadapt print out the alignment matrix.

v1.8.3 (2015-07-29)

• Fix issue #95: Untrimmed reads were not listed in the info file.
• Fix issue #138: pip install cutadapt did not work with new setuptools versions.
• Fix issue #137: Avoid a hang when writing to two or more gzip-compressed output files in Python 2.6.

v1.8.2 (2015-07-24)

v1.8.1 (2015-04-09)

• Fix #110: Counts for 'too short' and 'too long' reads were swapped in statistics.
• Fix #115: Make --trim-n work also on second read for paired-end data.

v1.8 (2015-03-14)

• Support single-pass paired-end trimming with the new -A/-G/-B/-U parameters. These work just like their -a/-g/-b/-u counterparts, but they specify sequences that are removed from the second read in a pair.

  Also, if you start using one of those options, the read modification options such as -q (quality trimming) are applied to both reads. For backwards compatibility, read modifications are applied to the first read only if neither of -A/-G/-B/-U is used. See the documentation for details.

  This feature has not been extensively tested, so please give feedback if something does not work.

• The report output has been re-worked in order to accomodate the new paired-end trimming mode. This also changes the way the report looks like in single-end mode. It is hopefully now more accessible.

• Chris Mitchell contributed a patch adding two new options: --trim-n removes any N bases from the read ends, and the --max-n option can be used to filter out reads with too many N.

• Support notation for repeated bases in the adapter sequence: Write A{10} instead of AAAAAAAAAA. Useful for poly-A trimming: Use -a A{100} to get the longest possible tail.

• Quality trimming at the 5' end of reads is now supported. Use -q 15,10 to trim the 5' end with a cutoff of 15 and the 3' end with a cutoff of 10.

• Fix incorrectly reported statistics (> 100% trimmed bases) when --times set to a value greater than one.

• Support .xz-compressed files (if running in Python 3.3 or later).

• Started to use the GitHub issue tracker instead of Google Code. All old issues have been moved.

v1.7 (2014-11-25)

• IUPAC characters are now supported. For example, use -a YACGT for an adapter that matches both CACGT and TACGT with zero errors. Disable with -N. By default, IUPAC characters in the read are not interpreted in order to avoid matches in reads that consist of many (low-quality) N bases. Use --match-read-wildcards to enable them also in the read.
• Support for demultiplexing was added. This means that reads can be written to different files depending on which adapter was found. See the section in the documentation for how to use it. This is currently only supported for single-end reads.
• Add support for anchored 3' adapters. Append $ to the adapter sequence to force the adapter to appear in the end of the read (as a suffix). Closes issue #81.
• Option --cut (-u) can now be specified twice, once for each end of the read. Thanks to Rasmus Borup Hansen for the patch!
• Options --minimum-length/--maximum-length (-m/-M) can be used standalone. That is, cutadapt can be used to filter reads by length without trimming adapters.
• Fix bug: Adapters read from a FASTA file can now be anchored.

v1.6 (2014-10-07)

• Fix bug: Ensure --format=... can be used even with paired-end input.
• Fix bug: Sometimes output files would be incomplete because they were not closed correctly.
• Alignment algorithm is a tiny bit faster.
• Extensive work on the documentation. It's now available at https://cutadapt.readthedocs.org/ .
• For 3' adapters, statistics about the bases preceding the trimmed adapter are collected and printed. If one of the bases is overrepresented, a warning is shown since this points to an incomplete adapter sequence. This happens, for example, when a TruSeq adapter is used but the A overhang is not taken into account when running cutadapt.
• Due to code cleanup, there is a change in behavior: If you use --discard-trimmed or --discard-untrimmed in combination with --too-short-output or --too-long-output, then cutadapt now writes also the discarded reads to the output files given by the --too-short or --too-long options. If anyone complains, I will consider reverting this.
• Galaxy support files are now in a separate repository.

v1.5 (2014-08-05)

• Adapter sequences can now be read from a FASTA file. For example, write -a file:adapters.fasta to read 3' adapters from adapters.fasta. This works also for -b and -g.
• Add the option --mask-adapter, which can be used to not remove adapters, but to instead mask them with N characters. Thanks to Vittorio Zamboni for contributing this feature!
• U characters in the adapter sequence are automatically converted to T.
• Do not run Cython at installation time unless the --cython option is provided.
• Add the option -u/--cut, which can be used to unconditionally remove a number of bases from the beginning or end of each read.
• Make --zero-cap the default for colorspace reads.
• When the new option --quiet is used, no report is printed after all reads have been processed.
• When processing paired-end reads, cutadapt now checks whether the reads are properly paired.
• To properly handle paired-end reads, an option --untrimmed-paired-output was added.

v1.4 (2014-03-13)

• This release of cutadapt reduces the overhead of reading and writing files. On my test data set, a typical run of cutadapt (with a single adapter) takes 40% less time due to the following two changes.
• Reading and writing of FASTQ files is faster (thanks to Cython).
• Reading and writing of gzipped files is faster (up to 2x) on systems where the gzip program is available.
• The quality trimming function is four times faster (also due to Cython).
• Fix the statistics output for 3' colorspace adapters: The reported lengths were one too short. Thanks to Frank Wessely for reporting this.
• Support the --no-indels option. This disallows insertions and deletions while aligning the adapter. Currently, the option is only available for anchored 5' adapters. This fixes issue 69.
• As a sideeffect of implementing the --no-indels option: For colorspace, the length of a read (for --minimum-length and --maximum-length) is now computed after primer base removal (when --trim-primer is specified).
• Added one column to the info file that contains the name of the found adapter.
• Add an explanation about colorspace ambiguity to the README

v1.3 (2013-11-08)

• Preliminary paired-end support with the --paired-output option (contributed by James Casbon). See the README section on how to use it.
• Improved statistics.
• Fix incorrectly reported amount of quality-trimmed Mbp (issue 57, fix by Chris Penkett)
• Add the --too-long-output option.
• Add the --no-trim option, contributed by Dave Lawrence.
• Port handwritten C alignment module to Cython.
• Fix the --rest-file option (issue 56)
• Slightly speed up alignment of 5' adapters.
• Support bzip2-compressed files.

v1.2 (2012-11-30)

• At least 25% faster processing of .csfasta/.qual files due to faster parser.
• Between 10% and 30% faster writing of gzip-compressed output files.
• Support 5' adapters in colorspace, even when no primer trimming is requested.
• Add the --info-file option, which has a line for each found adapter.
• Named adapters are possible. Usage: -a My_Adapter=ACCGTA assigns the name "My_adapter".
• Improve alignment algorithm for better poly-A trimming when there are sequencing errors. Previously, not the longest possible poly-A tail would be trimmed.
• James Casbon contributed the --discard-untrimmed option.

v1.1 (2012-06-18)

• Allow to "anchor" 5' adapters (-g), forcing them to be a prefix of the read. To use this, add the special character ^ to the beginning of the adapter sequence.
• Add the "-N" option, which allows 'N' characters within adapters to match literally.
• Speedup of approx. 25% when reading from .gz files and using Python 2.7.
• Allow to only trim qualities when no adapter is given on the command-line.
• Add a patch by James Casbon: include read names (ids) in rest file
• Use nosetest for testing. To run, install nose and run "nosetests".
• When using cutadapt without installing it, you now need to run bin/cutadapt due to a new directory layout.
• Allow to give a colorspace adapter in basespace (gets automatically converted).
• Allow to search for 5' adapters (those specified with -g) in colorspace.
• Speed up the alignment by a factor of at least 3 by using Ukkonen's algorithm. The total runtime decreases by about 30% in the tested cases.
• allow to deal with colorspace FASTQ files from the SRA that contain a fake additional quality in the beginning (use --format sra-fastq)

v1.0 (2011-11-04)

• ASCII-encoded quality values were assumed to be encoded as ascii(quality+33). With the new parameter --quality-base, this can be changed to ascii(quality+64), as used in some versions of the Illumina pipeline. (Fixes issue 7.)
• Allow to specify that adapters were ligated to the 5' end of reads. This change is based on a patch contributed by James Casbon.
• Due to cutadapt being published in EMBnet.journal, I found it appropriate to call this release version 1.0. Please see http://journal.embnet.org/index.php/embnetjournal/article/view/200 for the article and I would be glad if you cite it.
• Add Galaxy support, contributed by Lance Parsons.
• Patch by James Casbon: Allow N wildcards in read or adapter or both. Wildcard matching of 'N's in the adapter is always done. If 'N's within reads should also match without counting as error, this needs to be explicitly requested via --match-read-wildcards.

v0.9.5 (2011-07-20)

• Fix issue 20: Make the report go to standard output when -o/--output is specified.

• Recognize .fq as an extension for FASTQ files

• many more unit tests

• The alignment algorithm has changed. It will now find some adapters that previously were missed. Note that this will produce different output than older cutadapt versions!

  Before this change, finding an adapter would work as follows:

  • Find an alignment between adapter and read -- longer alignments are better.
  • If the number of errors in the alignment (divided by length) is above the maximum error rate, report the adapter as not being found.

  Sometimes, the long alignment that is found had too many errors, but a shorter alignment would not. The adapter was then incorrectly seen as "not found". The new alignment algorithm checks the error rate while aligning and only reports alignments that do not have too many errors.

v0.9.4 (2011-05-20)

• now compatible with Python 3
• Add the --zero-cap option, which changes negative quality values to zero. This is a workaround to avoid segmentation faults in BWA. The option is now enabled by default when --bwa/--maq is used.
• Lots of unit tests added. Run them with cd tests && ./tests.sh.
• Fix issue 16: --discard-trimmed did not work.
• Allow to override auto-detection of input file format with the new -f/--format parameter. This mostly fixes issue 12.
• Don't break when input file is empty.

v0.9.2 (2011-03-16)

• Install a single cutadapt Python package instead of multiple Python modules. This avoids cluttering the global namespace and should lead to less problems with other Python modules. Thanks to Steve Lianoglou for pointing this out to me!
• ignore case (ACGT vs acgt) when comparing the adapter with the read sequence
• .FASTA/.QUAL files (not necessarily colorspace) can now be read (some 454 software uses this format)
• Move some functions into their own modules
• lots of refactoring: replace the fasta module with a much nicer seqio module.
• allow to input FASTA/FASTQ on standard input (also FASTA/FASTQ is autodetected)

v0.9 (2011-01-10)

• add --too-short-output and --untrimmed-output, based on patch by Paul Ryvkin (thanks!)
• add --maximum-length parameter: discard reads longer than a specified length
• group options by category in --help output
• add --length-tag option. allows to fix read length in FASTA/Q comment lines (e.g., length=123 becomes length=58 after trimming) (requested by Paul Ryvkin)
• add -q/--quality-cutoff option for trimming low-quality ends (uses the same algorithm as BWA)
• some refactoring
• the filename - is now interpreted as standard in or standard output

v0.8 (2010-12-08)

• Change default behavior of searching for an adapter: The adapter is now assumed to be an adapter that has been ligated to the 3' end. This should be the correct behavior for at least the SOLiD small RNA protocol (SREK) and also for the Illumina protocol. To get the old behavior, which uses a heuristic to determine whether the adapter was ligated to the 5' or 3' end and then trimmed the read accordingly, use the new -b (--anywhere) option.
• Clear up how the statistics after processing all reads are printed.
• Fix incorrect statistics. Adapters starting at pos. 0 were correctly trimmed, but not counted.
• Modify scoring scheme: Improves trimming (some reads that should have been trimmed were not). Increases no. of trimmed reads in one of our SOLiD data sets from 36.5 to 37.6%.
• Speed improvements (20% less runtime on my test data set).

v0.7 (2010-12-03)

• Useful exit codes
• Better error reporting when malformed files are encountered
• Add --minimum-length parameter for discarding reads that are shorter than a specified length after trimming.
• Generalize the alignment function a bit. This is preparation for supporting adapters that are specific to either the 5' or 3' end.
• pure Python fallback for alignment function for when the C module cannot be used.

v0.6 (2010-11-18)

• Support gzipped input and output.
• Print timing information in statistics.

v0.5 (2010-11-17)

• add --discard option which makes cutadapt discard reads in which an adapter occurs

v0.4 (2010-11-17)

• (more) correctly deal with multiple adapters: If a long adapter matches with lots of errors, then this could lead to a a shorter adapter matching with few errors getting ignored.

v0.3 (2010-09-27)

• fix huge memory usage (entire input file was unintentionally read into memory)

v0.2 (2010-09-14)

• allow FASTQ input

v0.1 (2010-09-14)

• initial release