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.
  
• 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 v2.9.0 - 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

Links

OS	Arch	File, 中国镜像	Download Count
Linux	32-bit	seqkit_linux_386.tar.gz, 中国镜像
Linux	64-bit	seqkit_linux_amd64.tar.gz, 中国镜像
Linux	arm64	seqkit_linux_arm64.tar.gz, 中国镜像
macOS	64-bit	seqkit_darwin_amd64.tar.gz, 中国镜像
macOS	arm64	seqkit_darwin_arm64.tar.gz, 中国镜像
Windows	32-bit	seqkit_windows_386.exe.tar.gz, 中国镜像
Windows	64-bit	seqkit_windows_amd64.exe.tar.gz, 中国镜像

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 !!!

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.

SeqKit v2.6.0

Changes

• SeqKit v2.6.0 - 2023-11-09
  • seqkit:
    • add the shortcut -X for the flag --infile-list.
  • seqkit common:
    • add a new flag -e/--check-embedded-seqs for detecting embedded sequences.
    • for matching by sequences: reduced the memory occupation and corrected numbers in the log. #416
  • seqkit stat:
    • add a new column AvgQual for average quality score. #411
  • seqkit split2:
    • fix the panic for invalid input.
  • seqkit subseq:
    • add a new flag -R/--region-coord for appending coordinates to sequence ID for -r/--region. #413
  • seqkit locate:
    • add a new flag -s/--max-len-to-show to show at most X characters for the search pattern or matched sequences.
  • seqkit seq:
    • change the nucleotide color theme. #412

SeqKit v2.5.1

Changes

• SeqKit v2.5.1 - 2023-08-09
  • seqkit stats:
    • fix a concurrency bug (file name error) introduced in v2.5.0. #405
  • seqkit subseq:
    • sequence/chromosome IDs are case-sensitive now. #400

SeqKit v2.5.0

Changes

• SeqKit v2.5.0 - 2023-07-16
  • new command seqkit merge-slides: merge sliding windows generated from seqkit sliding. #390
  • seqkit stats:
    • added a new flag -N/--N for appending other N50-like stats as new columns. #393
    • added a progress bar for > 1 input files.
    • write the result of each file immediately (no output buffer) when using -T/--tabular.
  • seqkit translate:
    • add options -s/--out-subseqs and -m/--min-len to write ORFs longer than x amino acids as individual records. #389
  • seqkit sum:
    • do not remove possible '*' by default and delete confusing warnings. Thanks to @photocyte. #399
    • added a progress bar for > 1 input files.
  • seqkit pair:
    • remove the restriction of requiring FASTQ format, i.e., FASTA files are also supported.
  • seqkit seq:
    • update help messages. #387
  • seqkit fxtab:
    • faster alphabet computation (-a/--alphabet) with a new data structure. Thanks to @elliotwutingfeng #388
  • seqkit subseq:
    • accept reverse coordinates in BED/GTF. #392

SeqKit v2.4.0

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").