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@markschl markschl released this 14 Aug 14:22
· 181 commits to main since this release

Binary renamed: The binary was renamed from seqtool to st, because
typing the rather long name repeatedly can be tiring (-: The documentation
was updated accordingly

New commands:

  • view command for viewing sequences in terminal with colored background

Changes / additions:

  • Seqtool now handles quality scores associated with sequences. This includes:

    • Support for converting between FASTQ format variants
    • The exp_err statistics variable, which represents the total number of expected
      errors in a sequence, according to the quality scores. This allows filtering
      by sequence quality as done by fastq_filter from USEARCH and VSEARCH
    • 454-style QUAL files can be read an written
  • --format renamed to --fmt, and --outformat renamed to --to

  • The former txt format is now tsv (including the option --to-tsv).

Bug fixes:

  • seq_io was updated, containing two small bug fixes. Both bugs were very
    unlikely to be hit and of low severity