SeqKit v0.9.0-dev

@shenwei356 shenwei356 released this Aug 6, 2018 · 1 commit to master since this release

Changelog

  • seqkit: better handle of empty file, no error message shown. #36
  • new subcommand seqkit split2: split sequences into files by size/parts (FASTA, PE/SE FASTQ). #35

SeqKit v0.8.1

@shenwei356 shenwei356 released this Jun 29, 2018 · 3 commits to master since this release

Changlog

SeqKit v0.8.1
Github Releases (by Release)

  • seqkit: do not call pigz or gzip for decompressing gzipped file any more. But you can still utilize pigz or gzip by pigz -d -c seqs.fq.gz | seqkit xxx.
  • seqkit subseq: fix bug of missing quality when using --gtf or --bed
  • seqkit stats: parallelize counting files, it's much faster for lots of small files, especially for files on SSD

Please cite

W Shen, S Le, Y Li*, F Hu*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation.
PLOS ONE. doi:10.1371/journal.pone.0163962.

Links

Tips

  • run seqkit version to check update !!!
  • run seqkit genautocomplete to update Bash completion !!!
OS Arch File, 中国镜像 Download Count
Linux 32-bit seqkit_linux_386.tar.gz,
中国镜像
Github Releases (by Asset)
Linux 64-bit seqkit_linux_amd64.tar.gz,
中国镜像
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OS X 32-bit seqkit_darwin_386.tar.gz,
中国镜像
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OS X 64-bit seqkit_darwin_amd64.tar.gz,
中国镜像
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Windows 32-bit seqkit_windows_386.exe.tar.gz,
中国镜像
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Windows 64-bit seqkit_windows_amd64.exe.tar.gz,
中国镜像
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SeqKit v0.8.0

@shenwei356 shenwei356 released this Mar 22, 2018 · 6 commits to master since this release

Changelog

SeqKit v0.8.0Github Releases (by Release)

  • seqkit, stricter FASTA/Q format requirement, i.e., must starting with > or @.
  • seqkit, fix output format for FASTQ files containing zero-length records, yes this happens.
  • seqkit, add amino acid code O (pyrrolysine) and U (selenocysteine).
  • seqkit replace, add flag --nr-width to fill leading 0s for {nr}, useful for preparing sequence submission (">strain_00001 XX", ">strain_00002 XX").
  • seqkit subseq, require BED file to be tab-delimited.

SeqKit v0.7.2

@shenwei356 shenwei356 released this Dec 3, 2017 · 14 commits to master since this release

Changelog

SeqKit v0.7.2
Github Releases (by Release)

  • seqkit tab2fx: fix a concurrency bug that occurs in low proprobability when only 1-column data provided.
  • seqkit stats: add quartiles of sequence length
  • seqkit faidx: add support for retrieving subsequence using seq ID and region, which is similar with "samtools faidx" but has some extra features

SeqKit v0.7.1

@shenwei356 shenwei356 released this Sep 22, 2017 · 18 commits to master since this release

Changelog

SeqKit v0.7.1 Github Releases (by Release)

  • seqkit convert: fix bug of read quality containing only 3 or less values. shenwei356/bio/issues/3
  • seqkit stats: add option -T/--tabular to output in machine-friendly tabular format. #23
  • seqkit common: increase speed and decrease memory occupation, and add some notes.
  • fix some typos. #22
  • suggestion: please install pigz to gain better parsing performance for gzipped data.