SeqKit v2.12.0

Changes

• SeqKit v2.12.0 - 2025-12-04
  • seqkit grep:
    • -p/--pattern accepts empty character ("") now. So it's able to search records with empty IDs or sequences. #558
  • seqkit split2:
    • fix a bug introduced in v2.11.0: --by-part-prefix options has no effect. #554
  • seqkit replace:
    • {uuid}: use the time-sortable UUIDv7 to replace v4.
  • seqkit stats/fx2tab:
    • add information about how the average quality is computed. #448

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 !!!

SeqKit v2.11.0

Changes

• SeqKit v2.11.0 - 2025-11-20
  • seqkit:
    • fix reading records with both empty ID and sequence. #550
    • check if the output file name equals one of the input files. #541
  • seqkit split2:
    • add a new flag -N, --seqid-as-filename to use the first sequence ID as the file name.
      E.g., using -N -s 1 is equal to seqkit split --by-id, but it's much faster and uses less memory.
  • seqkit head:
    • add a new flag -l, --length to print heading FASTA/Q records with total sequence length >= N, e.g., -l 2G.
  • seqkit replace:
    • add a new replacement symbol {uuid} for random UUID. #552

SeqKit v2.10.1

Changes

• SeqKit v2.10.1 - 2025-08-19
  • seqkit seq:
    • fix validating sequences: it failed to report an error when the invalid sequence is not the last one in the input. #536
  • seqkit stats:
    • fix decimal places of some fields when using -T.
  • seqkit fx2tab:
    • fix the calculation of GC content (--gc). Previously, the denominator was the total sequence length, which could lead to inaccuracies due to the potential presence of gaps in the sequence. #515
  • seqkit sample:
    • fix -n for in-memory mode. #518
  • seqkit subseq:
    • fix the bug that subseq --feature is not case insensitive. #523
  • seqkit grep/locate/mutate:
    • update help message for -p/--pattern, to show how to set multiple values. #527 by @corneliusroemer

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 !!!

Please cite

Wei Shen*, Botond Sipos, and Liuyang Zhao. 2024. SeqKit2: A Swiss Army Knife for Sequence and Alignment Processing. iMeta e191. doi:10.1002/imt2.191.

SeqKit v2.10.0

Changes

• SeqKit v2.10.0 - 2025-03-12
  • seqkit:
    • add a global flag --skip-file-check: skip input file checking when given a file list if you believe these files do exist.
      It helps to reduce file checking time when given a huge number of sequence files.
  • seqkit split2:
    • fix prefix checking when paired-end files are given. #512
  • seqkit stat:
    • do not compute GC content and N's for protein sequence. #497
  • seqkit grep:
    • add early exit for --delete-matched when no patterns remain #505 by @sawyerknoblich
  • seqkit concat:
    • add an option -F/--fill to use a sequence of "-" for IDs missing in some files, can be used in MSA results. #510

SeqKit v2.9.0

Please cite:

• Wei Shen*, Botond Sipos, and Liuyang Zhao. 2024. SeqKit2: A Swiss Army Knife for Sequence and Alignment Processing. iMeta e191. doi:10.1002/imt2.191.
  

Changes

• SeqKit v2.9.0 - 2024-11-01
  • seqkit:
    • Fix sequence ID parsing with the default regular expression (in this case, we actually use bytes.Index instead) for a rare case: "xxx\tyyy zzz" was wrongly parsed as "xxx\tyyy". #486
  • seqkit locate:
    • Fix -G/--non-greedy for tandem repeats, e.g., ATTCGATTCGATTCG (ATTCGx3).
  • seqkit grep/subseq:
    • Fix negative regions longer than sequence length. #479.
  • seqkit stats:
    • Add an extra column sum_n to count the number of ambiguous characters. #490

SeqKit v2.8.2

Please cite:

1. Wei Shen*, Botond Sipos, and Liuyang Zhao. 2024. SeqKit2: A Swiss Army Knife for Sequence and Alignment Processing. iMeta e191. doi:10.1002/imt2.191.
   
2. Wei Shen, Shuai Le, Yan Li*, and Fuquan Hu*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation.
   PLOS ONE. doi:10.1371/journal.pone.0163962.
   

Changes

• SeqKit v2.8.2 - 2024-05-17
  • seqkit amplicon:
    • Fix a big introduced in v2.7.0. When more than one pairs of primers are given, only the last one is used. #457
  • seqkit translate:
    • Add option -e/--skip-translate-errors to skip translate error and output empty sequence. #458
  • seqkit split:
    • Add flag -I/--ignore-case for -i/--by-id. #462

SeqKit v2.8.1

Notice: I forgot to update the version number, so seqkit version will return 2.8.0.

Changelog

• SeqKit v2.8.1 - 2024-04-07
  • seqkit sana:
    • Add support for FASTQ files with IDs in the separator (+, 3rd) lines.. #446, #429, #408
  • seqkit subseq:
    • Add some docs to show how to keep the original order of sequences when extracting with BED: compress the input FASTA file. #451

SeqKit v2.8.0

Changelog

• SeqKit v2.8.0 - 2024-03-11
  • seqkit stats:
    • Add column N50_num, an alias of L50, #15.
  • seqkit seq/locate/fish/watch:
    • Removing the flag -V/--validate-seq-length. Now the whole sequence will be checked if -v/--validate-seq is given.
  • seqkit amplicon:
    • Fix the speed problem, introduced in v2.7.0. #439.
    • Slightly faster by reusing objects.
  • seqkit seq:
    • Change the threshold sequence length for parallelizing complement sequence computation, 1kb->1Mb.

SeqKit v2.7.0

Current Version

• SeqKit v2.7.0 - 2024-01-31
  • seqkit:
    • Grouping subcommands in help message, which is intuitive for beginners.
  • seqkit grep:
    • New flag: -D/--allow-duplicated-patterns for outputting records multiple times when duplicated patterns are given. #427
  • seqkit subseq:
    • Use the ID regular expression from the option --id-regexp to create FASTA index file. This solves the panic happened for sequences containing tabs in the headers. #432
  • seqkit split/sort/shuffle:
    • When using the two-pass mode (-2/--two-pass), replace possible tabs in the sequence header.
  • seqkit rmdup:
    • Write an empty file of duplicate numbers and lists of IDs even if there's no duplicates when using -D/--dup-num-file. #436
  • seqkit stats:
    • New flag -S/--skip-file-check to skip input file checking when given files or a file list. It's very useful if you run it with millions of files.

SeqKit v2.6.1

Changelog

• SeqKit v2.6.1 - 2023-11-18
  • seqkit:
    • fix panic of nil pointer introduced in v2.6.0, which happens when handling multiple input files and some of them have file sizes of zero.
  • seqkit seq:
    • fix panic (close of closed channel) when using -v to checking sequences.