SeqKit v2.13.0 (10-year-old birthday version)

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 !!!