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Published March 17, 2023 | Version v2.4.0
Software Open

shenwei356/seqkit: SeqKit v2.4.0

Creators

  • 1. Chongqing Medical University
  • 2. @nanoporetech
  • 3. @nanoporetech, @epi2me-labs
  • 4. EMBL-EBI
  • 5. Sun Yat-sen University Cancer center
  • 6. @meetup

Description

Changes
  • SeqKit v2.4.0 - 2023-03-17
    • seqkit:
      • support bzip2 format. #361
      • support setting compression level for gzip, zstd, and bzip2 format via --compress-level. #320
      • the global flag --infile-list accepts stdin (-) now.
      • wrap the help message of flags.
    • seqkit locate:
      • do not remove embeded regions when searching with regular expressions. #368
    • seqkit amplicon:
      • fix BED coordinates for amplicons found in the minus strand. #367
    • seqkit split:
      • fix forgetting to add extension for --two-pass. #332
    • seqkit stats:
      • fix compute Q1 and Q3 of sequence length for one record. #353
    • seqkit grep:
      • fix count number (-C) for matching with mismatch (-m > 0). #370
    • seqkit replace:
      • add some flags to match partly records to edit; these flags are transplanted from seqkit grep. #348
    • seqkit faidx:
      • allow empty lines at the end of sequences.
    • seqkit faidx/sort/shuffle/split/subseq:
      • new flag -U/--update-faidx: update the FASTA index file if it exists, to guarantee the index file matches the FASTA files. #364
      • improve log info and update help message. #365
    • seqkit seq:
      • allow filtering sequences of length zero. thanks to @penglbio.
    • seqkit rename:
      • new flag -s/--separator for setting separator between original ID/name and the counter (default "_"). #360
      • new flag -N/--start-num for setting starting count number for duplicated IDs/names (default 2). #360
      • new flag -1/--rename-1st-rec for renaming the first record as well. #360
      • do not append space if there's no description after the sequene ID.
    • seqkit sliding:
      • new flag -S/--suffix for change the suffix added to the sequence ID (default: "_sliding").
Links
OS Arch File, 中国镜像 Download Count
Linux 32-bit seqkit_linux_386.tar.gz, <br/> 中国镜像
Linux 64-bit seqkit_linux_amd64.tar.gz, <br/> 中国镜像
Linux arm64 seqkit_linux_arm64.tar.gz, <br/> 中国镜像
macOS 64-bit seqkit_darwin_amd64.tar.gz, <br/> 中国镜像
macOS arm64 seqkit_darwin_arm64.tar.gz, <br/> 中国镜像
Windows 32-bit seqkit_windows_386.exe.tar.gz, <br/> 中国镜像
Windows 64-bit seqkit_windows_amd64.exe.tar.gz, <br/> 中国镜像

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.

Notes

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

Files

shenwei356/seqkit-v2.4.0.zip

Files (34.1 MB)

Name Size Download all
md5:16bbb83486730330b5299f0b38fbe9e5
34.1 MB Preview Download

Additional details

Related works

Is supplement to
https://github.com/shenwei356/seqkit/tree/v2.4.0 (URL)