Releases | Open Source Science

vsearch - VSEARCH 2.30.0

Add options --n_mismatch, --fastq_minqual, and --fastq_truncee_rate.

The --n_mismatch option will count N's as mismatches in alignments, which may be useful to get sensible alignments for sequences with lots of N's. By default N's are counted as matches. Both the scoring and the counting of matches are affected.

The new --fastq_minqual option for the fastq_filter and fastx_filter commands will discard sequences with any nucleotide with a quality score below the given value. The new --fastq_truncee_rate option for the same commands will truncate sequences at the first position where the number of expected errors per base is below the given value.

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Published by torognes over 1 year ago

vsearch - VSEARCH 2.29.4

Adjust the window size used for chimera detection down from 64 to 32. The window size was by accident increased from 32 to 64 in version 2.23.0, leading to somewhat fewer chimeras being predicted. In addition, a compiler pragma has been included in align_simd.cc to further protect the compiler from generating wrong code.

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Published by torognes over 1 year ago

vsearch - VSEARCH 2.29.3

This version is released in order to mitigate a bug that occurs when compiling the align_simd.cc file on x8664 systems with the GNU C++ compiler version 9 or later with the -O3 optimization option. It results in incorrect code that may cause bad alignments in some circumstances. So far it has only been seen with the `allpairsglobalcommand. We are investigating this issue further, but for now we recommend compiling with the-O2` flag. The README.md file and the Dockerfiles have been updated to reflect this. The binaries released with this version will include this fix.

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Published by torognes over 1 year ago

vsearch - VSEARCH 2.29.2

Fix a segmentation fault during clustering when the set of clusters is empty. Initial documentation in markdown format available on GitHub Pages.

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Published by torognes over 1 year ago

vsearch - VSEARCH 2.29.1

Fix a segmentation fault that could occur during alignment in version 2.29.0, for example with --uchime_ref. Some improvements to code and documentation.

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Published by torognes over 1 year ago

vsearch - VSEARCH 2.29.0

vsearch 2.29.0 fixes seven bugs (see changelog below), adds initial support for RISC-V architectures, and improves code quality and code testing (1,210 new tests).

Changelog: - add: experimental support for RISCV64 and other 64-bit little-endian architectures, thanks to Michael R. Crusoe and his fellow Debian developers (PR #566), - add: official support for clang-19 and gcc 14, - add: beta support for clang-20, - remove: unused --output option for command --fastq_stats (issue #572), - fix: bug in --sintax when selecting the best lineage (only low confidence values below 0.5 were affected) (issue #573), - fix: out-of-bounds error in --fastq_stats when processing empty reads (issue #571), - fix: bug in --cut, patterns with multiple cutting sites were not detected (commit 4c4f9fa70f14b28d50185dbf322cf5727087e86a), - fix: memory error (segmentation fault) when using --derep_id and --strand (issue #565), - fix: --fastq_join now obeys to --quiet and --log options (commit 87f968b09f17c17ebf8db00aebe86e89b13a3948), - fix: --fastq_join quality padding is now also set to Q40 when quality offset is 64 (commit be0bf9b48d782286c4ce38f0bf1a4c82bd230250), - fix: (partial) --fastq_join's handling of abundance annotations (commit f2bbcb421dc2f4dfa6603b9f31ec3e4598c1b591), - improve: additional safeguards to validate input values and to make sure that they are within acceptable limits. Changes concern options --abskew (commit a530dd8990f8a05cb25fc0b6a5da5a14d28fbedd) and --fastq_maxdiffs (commit 4b254db7f120bfd49e86185ef3cd9070c236f940), - improve: code quality (1.3k+ commits, 6k+ clang-tidy warnings eliminated), - improve: documentation and help messages (issue #568), - improve: complete refactoring and modernization of a subset of commands (--sortbylength, --sortbysize, --shuffle, --rereplicate, --cut, --fastq_join, --fasta2fastq, --fastq_chars), - improve: code-coverage of our test-suite for the above-mentioned commands (1,210 new tests, 4,753 in total).

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Published by torognes almost 2 years ago

vsearch - VSEARCH 2.28.1

The sintax command has been improved in several ways in this version of vsearch. Please note that several details of this algorithm is not clearly described in the preprint, and the implementation in vsearch differs from that in usearch.

The former vsearch version did not always choose the most common taxonomic entity over the 100 bootstraps among the database sequences with the highest amount of word similarity to the query. Instead, if several sequences had an equal similarity with the query, the sequence encountered in the earliest bootstrap was chosen. The confidence level was calculated based on this sequence compared to the selected sequences from the other 99 bootstraps. This could lead to a suboptimal choice with a low confidence. In the new version, the most common of the sequences with the highest amount of word similarity across the 100 bootstraps will be selected, and ties will be broken randomly.

Another problem with the old implementation was that if several sequences had the same amount of word similarity, the shortest one in the reference database would be chosen, and if they were equally long, the earliest in the database file would be chosen. A new option called sintax_random has now been introduced. This option will randomly select one of the sequences with the highest number of shared words with the query, without considering their length or position. This avoids a bias towards shorter reference sequences. This option is strongly recommended and will probably soon be the default.

Furthermore, a ninth taxonomic rank, strain (letter t), is now recognized. The speed of the sintax command has also been significantly improved at least in some cases. Run vsearch with the randseed option and 1 thread to ensure reproducibility of the random choices in the algorithm.

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Published by torognes about 2 years ago

vsearch - VSEARCH 2.27.1

This version fixes the weak_id option and makes searches report weak hits in some cases. It also updates the names of the compression libraries to libz.so.1 and libbz2.so.1 on Linux to make them work on common Linux distributions without installing additional packages. README.md has been updated with information about compression libraries on Windows.

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Published by torognes about 2 years ago

vsearch - VSEARCH 2.27.0

The usearch_global and search_exact commands now support FASTQ files as well as FASTA files as input. This version of vsearch includes clarifications and updates to the manual. Some code has been refactored. Generic Dockerfiles for major Linux distributions have been included. Some warnings from compilers and other tools have been eliminated. The release for Windows will also include DLL's for the two compression libraries.

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Published by torognes over 2 years ago

vsearch - VSEARCH 2.26.1

Enable the maxseqlength and minseqlength options for the chimera detection commands. When the usearch_global or search_exact commands are used, OTU tables will include samples and OTUs with no matches.

The previous release 2.26.0 was removed because the version number had not been updated from 2.25.0 in the enclosed source code. To avoid confusion the previous release has been removed and replaced by this version 2.26.1.

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Published by torognes over 2 years ago

vsearch - VSEARCH 2.25.0

Allow a given percentage of mismatches, specified with the chimeras_diff_pct option, between chimeras and parents for the experimental chimeras_denovo command.

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Published by torognes over 2 years ago

vsearch - VSEARCH 2.24.0

Update documentation. Improve code. Allow up to 20 parents for the undocumented and experimental chimeras_denovo command. Fix compilation warnings for sha1.c. Compile for release (not debug) by default.

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Published by torognes over 2 years ago

vsearch - VSEARCH 2.23.0

Update documentation. Add citation file. Modernize and improve code. Fix several minor bugs. Fix compilation with GCC 13. Print stats after fastqmergepairs to log file instead of stderr. Handle sizein option correctly with dbmatched option for usearchglobal. Allow maxseqlength option for makeudbusearch. Fix memory allocation problem with chimera detection. Add lengthout and xlength options. Increase precision for eeout option. Add warning about sintax algorithm, random seed and multiple threads. Refactor chimera detection code. Add undocumented experimental longchimeras_denovo command. Fix segfault with clustering. Add more references.

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Published by torognes almost 3 years ago

vsearch - VSEARCH 2.22.1

Add the derep_smallmem command for dereplication with less memory usage. Remove compiler warnings.

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Published by torognes almost 4 years ago

vsearch - VSEARCH 2.21.2

Fix problems with the --lcaout option.

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Published by torognes almost 4 years ago

vsearch - VSEARCH 2.21.1

Fix dereplication with empty input file.

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Published by torognes over 4 years ago

vsearch - VSEARCH 2.21.0

This version adds the sample, qsegout and tsegout options. It also enables the use of UDB databases with uchime_ref.

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Published by torognes over 4 years ago

vsearch - VSEARCH 2.20.1

Fix hang in fastq_mergepairs with multiple threads.

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Published by torognes over 4 years ago

vsearch - VSEARCH 2.20.0

Added the fastx_uniques command and the fastq_qout_max option for dereplication of FASTQ files. Some code cleaning.

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Published by torognes over 4 years ago

vsearch - VSEARCH 2.19.0

Added the lcaout and lca_cutoff options to enable the output of last common ancestor (LCA) information about hits when searching. The randseed option was added as a valid option to the sintax command. Code improvements.

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Published by torognes over 4 years ago

vsearch - v2.18.0

Added the fasta2fastq command. Fixed search bug on ppc64le. Fixed bug with removal of size and ee info in uc files. Fixed compilation errors in some cases. Made some general code improvements. Updated manual.

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Published by torognes almost 5 years ago

vsearch - VSEARCH 2.17.1

Modernized code. Minor update to help info.

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Published by torognes about 5 years ago

vsearch - VSEARCH 2.17.0

The fastqmergepairs command has been changed. It now allows merging of sequences with overlaps as short as 5 bp if the --fastqminovlen option has been adjusted down from the default 10. In addition, much fewer pairs of reads should now be rejected with the reason 'multiple potential alignments' as the algorithm for detecting those have been changed. The orient command has also been improved.

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Published by torognes about 5 years ago

vsearch - VSEARCH 2.16.0

This version adds the orient command. It also handles empty input files properly. Documentation has been updated.

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Published by torognes over 5 years ago

vsearch - VSEARCH 2.15.2

No real functional changes, but some code and compilation changes. Code updated for C++11. Switch to C++ header files. Minor adaptations for Windows compatibility, including the use of the C++ standard library for regular expressions. Minor changes for compatibility with Power8. Compiles successfully on macOS running on Apple Silicon (ARMv8).

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Published by torognes over 5 years ago

vsearch - VSEARCH 2.15.1

Fix for derep_fulllength when including reverse complement sequences and headers. Make some extra checks when loading compression libraries and add more diagnostic output about them to the output of the version command. Report an error when fastx_filter is used with FASTA input and options that require FASTQ input. Update manual.

Added binary for macOS on Apple Silicon.

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Published by torognes over 5 years ago

vsearch - VSEARCH 2.15.0

Update manual and documentation. Turn on notrunclabels option for sintax command by default. Change maxhits 0 to mean unlimited hits, like the default. Allow non-ascii characters in headers, with a warning. Sort centroids and uc too when clusteroutsort specified. Add cluster id to centroids output when clusteroutid specified. Improve error messages when parsing FASTQ files. Add missing fastqqminout option and fix labelsuffix option for fastqmergepairs. Add derepid command that dereplicates based on both label and sequence. Remove compilation warnings.

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Published by torognes about 6 years ago

vsearch - VSEARCH 2.14.2

Fixed some issues with the cut, fastxrevcomp, fastqconvert, fastqmergepairs, and makeudbusearch commands. Updated manual.

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Published by torognes over 6 years ago

vsearch - VSEARCH 2.14.1

Fixed bug with sequences written to file specified with fastaoutrev for commands fastxfilter and fastq_filter.

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Published by torognes almost 7 years ago

vsearch - VSEARCH 2.14.0

Added relabelself option. Added fastawidth, sizein, sizeout and relabelling options as valid for certain commands.

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Published by torognes almost 7 years ago

vsearch - VSEARCH 2.13.7

Fixes a bug when generating consensus sequences.

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Published by torognes almost 7 years ago

vsearch - VSEARCH 2.13.6

Added info about the cut command to the output of the help command.

This should have been version 2.14.1 as it is a minor fix for version 2.13.5 which should have been version 2.14.0.

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Published by torognes almost 7 years ago

vsearch - VSEARCH 2.13.5

Added cut command to fragment sequences at restriction sites. Silenced output from the fastq_stats command if quiet option was given. Updated manual.

This should have been 2.14.0 as it is not just a bug fix, but adds new features.

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Published by torognes almost 7 years ago

vsearch - VSEARCH 2.13.4

Added information about support for gzip- and bzip2-compressed input files to the output of the version command. Adapted source code for compilation on FreeBSD and NetBSD systems.

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Published by torognes about 7 years ago

vsearch - VSEARCH 2.13.3

Fix bug in FASTQ parsing introduced in version 2.13.2.

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Published by torognes about 7 years ago

vsearch - VSEARCH 2.13.1

Minor changes to the allowed options for each command. All commands now allow the log, quiet and threads options. If more than 1 thread is specified for commands that are not multi-threaded, a warning will be issued. Minor changes to the manual.

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Published by torognes about 7 years ago

vsearch - VSEARCH 2.13.0

Added the fastx_getseq, fastx_getseqs and fastx_getsubseq commands to extract sequences from a FASTA or FASTQ file based on their labels. Improved handling of ambiguous nucleotide symbols. Corrected behaviour of uchime_ref command with and options self and selfid. Strict detection of illegal options for each command.

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Published by torognes about 7 years ago

vsearch - VSEARCH 2.12.0

Take sequence abundance into account when computing consensus sequences or profiles after clustering. Warn when rereplicating sequences without abundance info. Guess offset 33 in more cases withfastq_chars. Stricter checking of option arguments and option combinations.

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Published by torognes over 7 years ago

vsearch - VSEARCH 2.11.1

Minor change to the handling of the weakid and id options when using clusterunoise.

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Published by torognes over 7 years ago

vsearch - VSEARCH 2.11.0

Added ability to trim and filter paired-end reads using the reverse option with the fastx_filter and fastq_filter commands. Added xee option to remove ee attributes from FASTA headers. Minor invisible improvement to the progress indicator.

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Published by torognes over 7 years ago

vsearch - VSEARCH 2.10.4

Fixed serious bug in x8664 SIMD alignment code introduced in version 2.10.3. Added link to BioConda in README. Fixed bug in fastqstats with sequence length 1. Fixed use of equals symbol in UC files for identical sequences with cluster_fast.

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Published by torognes over 7 years ago

vsearch - VSEARCH 2.10.2

Fix bug in sintax with reversed order of domain and kingdom.

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Published by torognes over 7 years ago

vsearch - VSEARCH 2.10.1

Improved sff_convert command. It will now read several variants of the SFF format. It is also able to read from a pipe. Warnings are given if there are minor problems. Errors messages have been improved. Minor speed and memory usage improvements.

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Published by torognes over 7 years ago

vsearch - VSEARCH 2.10.0

Added the sff_convert command to convert SFF files to FASTQ.

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Published by torognes over 7 years ago

vsearch - VSEARCH 2.9.1

Fix illegal instruction error.

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Published by torognes over 7 years ago

vsearch - VSEARCH 2.9.0

Added the fastq_join command.

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Published by torognes over 7 years ago

vsearch - VSEARCH 2.8.6

Fixed bug in derep_fulllength causing headers not to be truncated after the first space. This bug was unfortunately introduced in version 2.8.2.

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Published by torognes over 7 years ago

vsearch - VSEARCH 2.8.5

Fix bug with fastq_eestats2.

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Published by torognes almost 8 years ago

vsearch - VSEARCH 2.8.4

Further reduce memory requirements for dereplication when not using the uc option. Fix output during subsampling when quiet or log options are in effect.

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Published by torognes almost 8 years ago

vsearch - VSEARCH 2.8.3

Fix for segfault bug with derep_fulllength and uc.

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Published by torognes almost 8 years ago

vsearch - VSEARCH 2.8.2

Fix for wrong placement of semicolons in header lines in some cases when using the sizeout or xsize options. Reduced memory requirements for full-length dereplication in cases with many duplicate sequences. Improved wording of fastq_mergepairs report. Updated manual regarding use of sizein and sizeout with dereplication. Changed a compiler option.

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Published by torognes almost 8 years ago

vsearch - VSEARCH 2.8.1

Fixes for compilation warnings with GCC 8.

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Published by torognes about 8 years ago

vsearch - VSEARCH 2.8.0

Added fastq_maxdiffpct option.

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Published by torognes about 8 years ago

vsearch - VSEARCH 2.7.1

Fixes several bugs on Windows.

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Published by torognes over 8 years ago

vsearch - VSEARCH 2.7.0

Added clusterunoise, uchime2denovo and uchime3_denovo commands.

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Published by torognes over 8 years ago

vsearch - VSEARCH 2.6.2

Fix for partially inactive xsize option.

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Published by torognes over 8 years ago

vsearch - VSEARCH 2.6.0

Rewritten paired-end reads merger with improved accuracy. Decreased default value for fastqminovlen option from 16 to 10. The default value for the fastqmaxdiffs option is increased from 5 to 10. There are now other more important restrictions that will avoid merging reads that cannot be reliably aligned.

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Published by torognes over 8 years ago

vsearch - VSEARCH 2.5.2

Fix bug with '-' not treated as stdin when used as argument to fastq_eestats2 option.

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Published by torognes over 8 years ago

vsearch - VSEARCH 2.5.1

Fixed bug with bad default value of 1 instead of 32 for minseqlength when using the makeudb_usearch command.

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Published by torognes over 8 years ago

vsearch - VSEARCH 2.5.0

Support for UDB database files. New commands: fastqstripright, fastqeestats2, makeudbusearch, udb2fasta, udbinfo, and udbstats. New general option: noprogress. New options minsize and maxsize to fastx_filter. Minor bug fixes, error message improvements and documentation updates.

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Published by torognes over 8 years ago

vsearch - VSEARCH 2.4.4

Several minor bug fixes, improved error messages and updated documentation.

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Published by torognes almost 9 years ago

vsearch - VSEARCH 2.4.3

Fixed bug with progress bar for shuffling. Fixed missing N-lines in UC files with usearchglobal, searchexact and allpairsglobal when the outputno_hits option was not specified.

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Published by torognes about 9 years ago

vsearch - VSEARCH 2.4.2

Default value for fastq_minovlen increased to 16 in accordance with help text and for compatibility with usearch. Minor changes for improved accuracy of paired-end read merging.

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Published by torognes over 9 years ago

vsearch - VSEARCH 2.4.1

This version fixes overflow bugs in fastqstats and fastqeestats with very large FASTQ files. It also fixes a memory reporting issue on Windows. Minor documentation updates.

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Published by torognes over 9 years ago

vsearch - VSEARCH 2.4.0

This release includes support for Linux on the Power8 architecture (using AltiVec) as well as Windows on x86_64. The documentation has been updated and a few small bugs have been corrected.

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Published by torognes over 9 years ago

vsearch - VSEARCH 2.3.4 Windows pre-release

This is a pre-release of VSEARCH 2.3.4 for 64-bit Windows. The binary is compiled with the mingw-w64 cross compiler. Not tested well. Not for production. Feel free to try it out!

For support for gzipped or bzip2'ed files you need the zlib1.dll or bz2.dll libraries.

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Published by torognes over 9 years ago

vsearch - VSEARCH 2.3.4

Fix bug in profile output, update docs. Solves issue #220.

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Published by torognes over 9 years ago

vsearch - VSEARCH 2.3.3

Minor speed improvements.

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Published by torognes over 9 years ago

vsearch - VSEARCH 2.3.2

Fix bug in column 2 of H-lines in UC output files after clustering. Resolves issue #207.

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Published by torognes over 9 years ago

vsearch - VSEARCH 2.3.1 Windows pre-release

This is a pre-release of VSEARCH 2.3.1 for 64-bit Windows. The binary is compiled with the mingw-w64 cross compiler. Not tested well. Not for production. Feel free to try it out!

For support for gzipped or bzip2'ed files you need the zlib1.dll or bz2.dll libraries.

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Published by torognes over 9 years ago

vsearch - VSEARCH 2.3.1

Fixed bug where --minwordmatches 0 was interpreted as the default minimum word matches for the given word length instead of zero. When used in combination with --maxaccepts 0 and --maxrejects 0 it will now allow complete bypass of the kmer-based heuristics.

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Published by torognes over 9 years ago

vsearch - VSEARCH 2.3.0

Allow zero-length sequences. New fastqtrunclenkeep option.

Tue 8 Nov: Updated linux binary by compiling with the older gcc 4.9.2 to avoid error message "/usr/lib/x8664-linux-gnu/libstdc++.so.6: version `GLIBCXX3.4.21' not found".

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Published by torognes over 9 years ago

vsearch - VSEARCH 2.2.0

Added options for OTU table generation: --biomout, --mothur_shared_out and --otutabout.

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Published by torognes over 9 years ago

vsearch - VSEARCH 2.1.2

Fixed incorrect abundance output from fastxfilter and fastqfilter when relabelling.

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Published by torognes over 9 years ago

vsearch - VSEARCH 2.1.1

Fixed bugs in UC-output from clustering, updated docs.

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Published by torognes almost 10 years ago

vsearch - VSEARCH 2.1.0

Added fastxfilter command and options fastqtruncee and fastq_maxlen. Allowed minwordmatches down to 3.

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Published by torognes almost 10 years ago

vsearch - VSEARCH 2.0.5

Added options to output discarded sequences from subsampling to separate files. Updated manual.

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Published by torognes almost 10 years ago

vsearch - VSEARCH 2.0.4

Improved manual and one error message.

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Published by torognes almost 10 years ago

vsearch - VSEARCH 2.0.3

Fix Illegal instruction faults when running the precompiled binaries on some systems.

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Published by torognes almost 10 years ago

vsearch - VSEARCH 2.0.2

Fix GCC version 6 warnings.

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Published by torognes almost 10 years ago

vsearch - VSEARCH 2.0.1

Fix segmentation fault when masking very long sequences, due to use of alloca.

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Published by torognes almost 10 years ago

vsearch - VSEARCH 2.0.0

Support for reading from and writing to pipes.

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Published by torognes about 10 years ago

vsearch - VSEARCH 1.11.2

Fixed issues relating to query_cov option and to consensus sequences with Ns.

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Published by torognes about 10 years ago

vsearch - VSEARCH 1.11.1

Add strand info to uc file after dereplication. Add info about expected errors (ee) to FASTA files with fastqfilter and fastqmergepairs commands if option -fastq_eeout or -eeout is specified. Delete unnecessary autotool files.

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Published by torognes about 10 years ago

vsearch - VSEARCH 1.10.2

Fixed a bug causing a segmentation fault when running usearch_global with an empty query sequence. Also fixed a bug causing imperfect alignments to be reported with an alignment string of "=" in uc output files. Fixed typos in man file. Fixed fasta/fastq processing code regarding presence or absence of compression library header files.