Published February 27, 2026 | Version v2.13.0
Software Open

shenwei356/seqkit: SeqKit v2.13.0 (10-year-old birthday version)

Authors/Creators

  • 1. Chongqing Medical University, China
  • 2. @nanoporetech
  • 3. @nanoporetech, @epi2me-labs
  • 4. @neherlab @nextstrain
  • 5. CNRS
  • 6. @justworkshr
  • 7. University of California, San Diego
  • 8. Karolinska University Hospital
  • 9. Sun Yat-sen University Cancer center
  • 10. Snap Inc.
  • 11. University of São Paulo

Description

Changelog

SeqKit is 10 years old!

  • SeqKit v2.13.0 - 2026-02-28
    • seqkit: add support for reading and writing LZ4 compression format.
    • new command: seqkit sample2: improved seqkit sample by @stahiga. #566, #386
    • seqkit seq:
      • add flags to specify sequences to operate/transform. #568
    • seqkit shuffle:
      • add a new option --tmp-dir, which can specify tmp dir for FASTA records from stdin or compressed FASTA files. #562
    • seqkit shuffle/sample:
      • add a new flag -r/--non-deterministic, which uses a time-based seed to generate non-deterministic (truly random) results. #565
    • seqkit restart:
      • support specifying the starting sequence of circular genomes.
    • seqkit split/split2:
      • add a new option -P/--out-prefix to override --by-*-prefix, for simplifying output prefix setting. #563
    • seqkit bam:
      • fix a bug #200 by @botond-sipos.
    • seqkit stats:
      • fix detecting file format type for FASTQ records with empty sequences. #569

Notes

  • please open an issue to request binaries for other platforms.
  • run seqkit version to check update !!!
  • run seqkit genautocomplete to update shell autocompletion script !!!

Files

shenwei356/seqkit-v2.13.0.zip

Files (34.3 MB)

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md5:9ef431e12ac871bb7ec5642a4d5ae3d1
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Additional details

Related works

Is supplement to
Software: https://github.com/shenwei356/seqkit/tree/v2.13.0 (URL)

Software

Repository URL
https://github.com/shenwei356/seqkit