Download

SeqKit is implemented in Go programming language, statically-linked executable binary files are freely available.

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.

Current Version

• 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 !!!

Installation

Method 1: Download binaries (latest stable version)

Just download compressed executable file of your operating system, and decompress it with tar -zxvf *.tar.gz command or other tools. And then:

1. For Linux-like systems

   1. If you have root privilege simply copy it to /usr/local/bin:

      sudo cp seqkit /usr/local/bin/
      

   2. Or copy to anywhere in the environment variable PATH:

      mkdir -p $HOME/bin/; cp seqkit $HOME/bin/
      

2. For windows, just copy seqkit.exe to C:\WINDOWS\system32.

Method 2: Install via conda (latest stable version)

conda install -c bioconda seqkit

Method 3: Install via homebrew (might not be latest stable version)

brew install seqkit

Method 4: For Go developer (latest stable/dev version)

go get -u github.com/shenwei356/seqkit/v2/seqkit/

Method 5: Docker based installation (might not be latest stable versio)

Install Docker

git clone this repo:

git clone https://github.com/shenwei356/seqkit

Run the following commands:

cd seqkit
docker build -t shenwei356/seqkit .
docker run -it shenwei356/seqkit:latest

Method 6: Compiling from source (latest stable/dev version)

# ------------------- install golang -----------------

# download Go from https://go.dev/dl
wget https://go.dev/dl/go1.17.13.linux-amd64.tar.gz

tar -zxf go1.17.13.linux-amd64.tar.gz -C $HOME/

# or 
#   echo "export PATH=$PATH:$HOME/go/bin" >> ~/.bashrc
#   source ~/.bashrc
export PATH=$PATH:$HOME/go/bin


# ------------- the latest stable version -------------

go get -v -u github.com/shenwei356/seqkit/seqkit

# The executable binary file is located in:
#   ~/go/bin/seqkit
# You can also move it to anywhere in the $PATH
mkdir -p $HOME/bin
cp ~/go/bin/seqkit $HOME/bin/

# --------------- the development version --------------

git clone https://github.com/shenwei356/seqkit
cd seqkit/seqkit/
go build

# The executable binary file is located in:
#   ./seqkit
# You can also move it to anywhere in the $PATH
mkdir -p $HOME/bin
cp ./seqkit $HOME/bin/

Shell-completion

Supported shell: bash|zsh|fish|powershell

Bash:

# generate completion shell
seqkit genautocomplete --shell bash

# configure if never did.
# install bash-completion if the "complete" command is not found.
echo "for bcfile in ~/.bash_completion.d/* ; do source \$bcfile; done" >> ~/.bash_completion
echo "source ~/.bash_completion" >> ~/.bashrc

Zsh:

# generate completion shell
seqkit genautocomplete --shell zsh --file ~/.zfunc/_seqkit

# configure if never did
echo 'fpath=( ~/.zfunc "${fpath[@]}" )' >> ~/.zshrc
echo "autoload -U compinit; compinit" >> ~/.zshrc

fish:

seqkit genautocomplete --shell fish --file ~/.config/fish/completions/seqkit.fish

Release history

• 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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").
• SeqKit v2.3.1 - 2022-09-22
  • seqkit grep/locate: fix bug of FMIndex building for empty sequences. #321
  • seqkit split2: fix bug of splitting two FASTA files. #325
  • seqkit faidx: --id-regexp works now.
• SeqKit v2.3.0 - 2022-08-12
  • seqkit grep/rename:
    • reduce memory comsumption for a lot of searching patterns, and it's faster. #305
    • 2X faster -s/--by-seq.
  • seqkit split
    • fix outputting an empty file when the number of sequence equal to the split size. #293
    • add options to set output file prefix and extention. #296
  • seqkit split2
    • reduce memory consumption. #304
    • add options to set output file prefix
  • seqkit stats:
    • add GC content. #294

• SeqKit v2.2.0 - 2020-03-14

  • seqkit:
    • add support of xz and zstd input/output formats. #274
    • fix panic when reading records with header of ID + blanks.
  • new command seqkit sum: computing message digest for all sequences in FASTA/Q files. The idea comes from @photocyte and the format borrows from seqhash #262
  • new command seqkit fa2fq: retrieving corresponding FASTQ records by a FASTA file
  • seqkit split2:
    • new flag -e/--extension for forcing compresson or changing compression format. #276
    • support changing output prefix via -o/--out-file. #275
  • seqkit concat:
    • fix handling of multiple seqs with the same ID in one file. #269
    • performaning out/full join. #270
    • preserve the comments. #271
  • seqkit locate:
    • parallelizing -F/--use-fmi and -m for large number of search patterns.
  • seqkit amplicon:
    • new flag -M/--output-mismatches to append the total mismatches and mismatches of 5' end and 3' end. #286
  • seqkit grep:
    • detect FASTA/Q symbol @ and > in the searching patterns and show warnings.
    • add new flag -C/--count, like grep -c in GNU grep. #267
  • seqkit range:
    • support removing leading 100 seqs (seqkit range -r 101:-1 == tail -n +101). #279
  • seqkit subseq:
    • report error when no options were given.
  • update doc:
    • seqkit head: add doc for "seqkit tail": seqkit range -N:-1 seqs.fasta. #272
    • seqkit rmdup: add the note of only the first record being saved for duplicates. #265

• SeqKit v2.1.0 - 2021-11-15

  • seqkit seq:
    • fix filtering by average quality -Q/-R. #257
  • seqkit convert:
    • fix quality encoding checking, change default value of -N/--thresh-B-in-n-most-common from 4 to 2. #254 and #239
  • seqkit split:
    • fix writing an extra empty file when using --two-pass#244
  • seqkit subseq:
    • fix --bed which fail to recognize strand ..
  • seqkit fq2fa:
    • faster, and do not wrap sequences.
  • seqkit grep/locate/mutate:
    • detect unquoted comma and show warning message, e.g., -p 'A{2,}'. #250
• SeqKit v2.0.0 - 2021-08-27
  • Performance improvements
    • seqkit:
      • faster FASTA/Q reading and writing, especially on FASTQ, see the benchmark.
        • reading (plain text): 4X faster. seqkit stats dataset_C.fq
        • reading (gzip files): 45% faster. seqkit stats dataset_C.fq.gz
        • reading + writing (plain text): 3.5X faster. seqkit grep -p . -v dataset_C.fq -o t
        • reading + writing (gzip files): 2.2X faster. seqkit grep -p . -v dataset_C.fq.gz -o t.gz
      • change default value of -j/--threads from 2 to 4, which is faster for writting gzip files.
    • seqkit seq:
      • fix writing speed, which was slowed down in v0.12.1.
  • Breaking changes
    • seqkit grep/rmdup/common:
      • consider reverse complement sequence by default for comparing by sequence, add flag -P/--only-positive-strand. #215
    • seqkit rename:
      • rename ID only, do not append original header to new ID. #236
    • seqkit fx2tab:
      • for -s/--seq-hash: outputing MD5 instead of hash value (integers) of xxhash. #219
  • Bugfixes
    • seqkit seq:
      • fix failing to output gzipped format for file name with extension of .gz since v0.12.1.
    • seqkit tab2fx:
      • fix bug for very long sequences. #214
    • seqkit fish:
      • fix range check. #213
    • seqkit grep:
      • it's not exactly a bug: forgot to use multi-threads for -m > 0.
  • New features/enhancements
    • seqkit grep:
      • allow empty pattern files.
    • seqkit faidx:
      • support region with begin > end, i.e., returning reverse complement sequence
      • add new flag -l/--region-file: file containing a list of regions.
    • seqkit fx2tab:
      • new flag -Q/--no-qual for disabling outputing quality even for FASTQ file. #221
    • seqkit amplicon:
      • new flag -u/--save-unmatched for saving records that do not match any primer.
    • seqkit sort:
      • new flag -b/--by-bases for sorting by non-gap bases, for multiple sequence alignment files.#216
• SeqKit v0.16.1 - 2021-05-20
  • seqkit shuffle --two-pass: fix bug introduced in #173 . #209
  • seqkit pair: fix a dangerous bug: when input files are not in current directory, input files were overwritten.
• SeqKit v0.16.0 - 2021-04-16
  • new command seqkit head-genome:
    • print sequences of the first genome with common prefixes in name
  • seqkit grep/locate/amplicon -m
    • much faster (300-400x) searching with mismatch allowed by optimizing FM-indexing and parallelization.
    • new flag -I/--immediate-output.
  • seqkit grep/locate:
    • fix bug of -m when querying contains letters not in alphabet, usually for protein sequences. #178, #179
    • onply search on positive strand when searching unlimited or protein sequences.
  • seqkit locate:
    • removing debug info for -r introduced in a0f6b6e. #180
  • seqkit amplicon:
    • fix bug of -m, when mismatch is allowed.
  • seqkit fx2tab:
    • new flag -C/--base-count for counting bases. #183
  • seqkit tab2fx:
    • fix a rare bug. #197
  • seqkit subseq:
    • fix bug for BED with empty columns. #195
  • seqkit genautocomplete:
    • support bash|zsh|fish|powershell.
• SeqKit v0.15.0 - 2021-01-12
  • seqkit grep/locate: update help message.
  • seqkit grep: search on both strand when searching by sequence.
  • seqkit split2: fix redundant log when using -s.
  • seqkit bam: new field RightSoftClipSeq. #172
  • seqkit sample -2: remove extra \n. #173
  • seqkit split2 -l: fix bug for splitting by accumulative length, this bug occurs when the first record is longer than -l, no sequences are lost.
• SeqKit v0.14.0 - 2020-10-30
  • new command seqkit pair: match up paired-end reads from two fastq files, faster than fastq-pair.
  • seqkit translate: new flag -F/--append-fram for optional adding frame info to ID. #159
  • seqkit stats: reduce memory usage when using -a for calculating N50. #153
  • seqkit mutate: fix inserting sequence -i/--insertion, this bug occurs when insert site is big in some cases, don't worry if no error reported.
  • seqkit replace:
    • new flag -U/--keep-untouched: do not change anything when no value found for the key (only for sequence name).
    • do no support editing FASTQ sequence.
  • seqkit grep/locate: new flag --circular for supporting circular genome. #158
• SeqKit v0.13.2 - 2020-07-13
  • seqkit sana: fix bug causing hanging on empty files. #149
• SeqKit v0.13.1 - 2020-07-09
  • seqkit sana: fix bug causing hanging on empty files. #148
• SeqKit v0.13.0 - 2020-07-07
  • seqkit: fix a rare FASTA/Q parser bug. #127
  • seqkit seq: output sequence or quality in single line when -s/--seq or -q/--qual is on. #132
  • seqkit translate: delete debug info, #133, and fix typo. #134
  • seqkit split2: tiny performance improvement. #137
  • seqkit stats: new flag -i/--stdin-label for replacing default "-" for stdin. #139
  • seqkit fx2tab: new flag -s/--seq-hash for printing hash of sequence (case sensitive). #144
  • seqkit amplicon:
    • fix bug of missing searching reverse strand. #140
    • supporting degenerate bases now. #83
    • new flag -p/--primer-file for reading list of primer pairs. #142
    • new flag --bed for outputing in BED6+1 format. #141
  • New features and improvements by @bsipos. #130, #147
    • new command seqkit scat, for real-time robust concatenation of fastx files.
    • Rewrote the parser behind the sana subcommand, now it supports robust parsing of fasta file as well.
    • Added a "toolbox" feature to the bam subcommand (-T), which is a collection of filters acting on streams of BAM records configured through a YAML string (see the docs for more).
    • Added the SEQKIT_THREADS environmental variable to override the default number of threads.
• SeqKit v0.12.1 - 2020-04-21
  • seqkit bam: add colorised and pretty printed output, by @bsipos. #110
  • seqkit locate/grep: fix bug of -m, when query contains letters not in subject sequences. #124
  • seqkit split2: new flag -l/--by-length for splitting into chunks of N bases.
  • seqkit fx2tab:
    • new flag -I/--case-sensitive for calculating case sensitive base content. #108
    • add missing column name for averge quality for -H -q. #115
    • fix output of -n/--only-name, do not write empty columns of sequence and quality. #104, #115
  • seqkit seq: new flag -k/--color: colorize sequences.
• SeqKit v0.12.0 - 2020-02-18
  • seqkit:
    • fix checking input file existence.
    • new global flag --infile-list for long list of input files, if given, they are appended to files from cli arguments.
  • seqkit faidx: supporting "truncated" (no ending newline charactor) file.
  • seqkit seq:
    • do not force switching on -g when using -m/-M.
    • show recommendation if flag -t/--seq-type is not DNA/RNA when computing complement sequence. #103
  • seqkit translate: supporting multiple frames. #96
  • seqkit grep/locate:
    • add detection and warning for space existing in search pattern/sequence.
    • speed improvement (2X) for -m/--max-mismatch. shenwei356/bwt/issues/3
  • seqkit locate:
    • new flag -M/--hide-matched for hiding matched sequences. #98
    • new flag -r/--use-regexp for explicitly using regular expression, so improve speed of default index operation. And you have to switch this on if using regexp now. #101
    • new flag -F/--use-fmi for improving search speed for lots of sequence patterns.
  • seqkit rename: making IDs unique across multiple files, and can write into multiple files. #100
  • seqkit sample: fix stdin checking for flag -2. #102.
  • seqkit rename/split/split2: fix detection of existed outdir.
  • split split: fix bug of seqkit split -i -2 and parallizing it.
  • seqkit version: checking update is optional (-u).
• SeqKit v0.11.0 - 2019-09-25
  • seqkit: fix hanging when reading from truncated gzip file.
  • new commands:
    • seqkit amplicon: retrieve amplicon (or specific region around it) via primer(s).
  • new commands by @bsipos:
    • seqkit watch: monitoring and online histograms of sequence features.
    • seqkit sana: sanitize broken single line fastq files.
    • seqkit fish: look for short sequences in larger sequences using local alignment.
    • seqkit bam: monitoring and online histograms of BAM record features.
  • seqkit grep/locate: reduce memory occupation when using flag -m/--max-mismatch.
  • seqkit seq: fix panic of computing complement sequence for long sequences containing illegal letters without flag -v on. #84
• SeqKit v0.10.2 - 2019-07-30
  • seqkit: fix bug of parsing sequence ID delimited by tab (\t). #78
  • seqkit grep: better logic of --delete-matched.
  • seqkit common/rmdup/split: use xxhash to replace MD5 when comparing with sequence, discard flag -m/--md5.
  • seqkit stats: new flag -b/--basename for outputting basename instead of full path.
• SeqKit v0.10.1 - 2019-02-27
  • seqkit fx2tab: new option -q/--avg-qual for outputting average read quality. #60
  • seqkit grep/locate: fix support of X when using -d/--degenerate. #61
  • seqkit translate:
    • new flag -M/--init-codon-as-M to translate initial codon at beginning to 'M'. #62
    • translates --- to - for aligned DNA/RNA, flag -X needed. #63
    • supports codons containing ambiguous bases, e.g., GGN->G, ATH->I. #64
    • new flag -l/--list-transl-table to show details of translate table N
    • new flag -l/--list-transl-table-with-amb-codons to show details of translate table N (including ambigugous codons)
  • seqkit split/split2, fix bug of ignoring -O when reading from stdin.
• SeqKit v0.10.0 - 2018-12-24
  • seqkit: report error when input is directory.
  • new command seqkit mutate: edit sequence (point mutation, insertion, deletion).
• SeqKit v0.9.3 - 2018-12-02
  • seqkit stats: fix panic for empty file. #57
  • seqkit translate: add flag -x/--allow-unknown-codon to translate unknown codon to X.
• SeqKit v0.9.2 - 2018-11-16
  • seqkit: stricter checking for value of global flag -t/--seq-type.
  • seqkit sliding: fix bug for flag -g/--greedy. #54
  • seqkit translate: fix bug for frame < 0. #55
  • seqkit seq: add TAB to default blank characters (flag -G/--gap-letters), and fix filter result when using flag -g/--remove-gaps along with -m/--min-len or -M/--max-len
• SeqKit v0.9.1 - 2018-10-12
  • seqkit faidx: fix bug of retrieving subsequence with multiple regions on same sequence. #48
  • seqkit sort/shuffle/split: fix bug when using -2/--two-pass to process .gz files. #52
• SeqKit v0.9.0 - 2018-09-26
  • seqkit: better handle of empty file, no error message shown. #36
  • new subcommand seqkit split2: split sequences into files by size/parts (FASTA, PE/SE FASTQ). #35
  • new subcommand seqkit translate: translate DNA/RNA to protein sequence. #28
  • seqkit sort: fix bug when using -2 -i, and add support for sorting in natural order. #39
  • seqkit grep and seqkit locate: add experimental support of mismatch when searching subsequences. #14
  • seqkit stats: add stats of Q20 and Q30 for FASTQ. #45
• SeqKit v0.8.1 - 2018-06-29
  • seqkit: do not call pigz or gzip for decompressing gzipped file any more. But you can still utilize pigz or gzip by pigz -d -c seqs.fq.gz | seqkit xxx.
  • seqkit subseq: fix bug of missing quality when using --gtf or --bed
  • seqkit stats: parallelize counting files, it's much faster for lots of small files, especially for files on SSD
• SeqKit v0.8.0 - 2018-03-22
• seqkit, stricter FASTA/Q format requirement, i.e., must starting with > or @.
• seqkit, fix output format for FASTQ files containing zero-length records, yes this happens.
• seqkit, add amino acid code O (pyrrolysine) and U (selenocysteine).
• seqkit replace, add flag --nr-width to fill leading 0s for {nr}, useful for preparing sequence submission (">strain_00001 XX", ">strain_00002 XX").
• seqkit subseq, require BED file to be tab-delimited.
• SeqKit v0.7.2 - 2017-12-03
  • seqkit tab2fx: fix a concurrency bug that occurs in low proprobability when only 1-column data provided.
  • seqkit stats: add quartiles of sequence length
  • seqkit faidx: add support for retrieving subsequence using seq ID and region, which is similar with "samtools faidx" but has some extra features
• SeqKit v0.7.1 - 2017-09-22
  • seqkit convert: fix bug of read quality containing only 3 or less values. shenwei356/bio/issues/3
  • seqkit stats: add option -T/--tabular to output in machine-friendly tabular format. #23
  • seqkit common: increase speed and decrease memory occupation, and add some notes.
  • fix some typos. #22
  • suggestion: please install pigz to gain better parsing performance for gzipped data.
• SeqKit v0.7.0 - 2017-08-12
  • add new command convert for converting FASTQ quality encoding between Sanger, Solexa and Illumina. Thanks suggestion from @cviner ( #18). usage & example.
  • add new command range for printing FASTA/Q records in a range (start:end). #19. usage & example.
  • add new command concate for concatenating sequences with same ID from multiple files. usage & example.
• SeqKit v0.6.0 - 2017-06-21
  • add new command genautocomplete to generate shell autocompletion script! (#17)
  • add new command seqkit dup for duplicating sequences (#16)
  • seqkit stats -a does not show L50 which may brings confusion (#15)
  • seqkit subseq --bed: more robust for bad BED files
• SeqKit v0.5.5 - 2017-05-10
  • Increasing speed of reading .gz file by utilizing gzip (1.3X), it would be much faster if you installed pigz (2X).
  • Fixing colorful output in Windows
  • seqkit locate: add flag --gtf and --bed to output GTF/BED6 format, so the result can be used in seqkit subseq.
  • seqkit subseq: fix bug of --bed, add checking coordinate.
• SeqKit v0.5.4 - 2017-04-11
  • seqkit subseq --gtf, add flag --gtf-tag to set tag that's outputted as sequence comment
  • fix seqkit split and seqkit sample: forget not to wrap sequence and quality in output for FASTQ format
  • compile with go1.8.1
• SeqKit v0.5.3 - 2017-04-01
  • seqkit grep: fix bug when using seqkit grep -r -f patternfile: all records will be retrived due to failing to discarding the blank pattern (""). #11
• SeqKit v0.5.2 - 2017-03-24
  • seqkit stats -a and seqkit seq -g -G: change default gap letters from '- ' to '- .'
  • seqkit subseq: fix bug of range overflow when using -d/--down-stream or -u/--up-stream for retieving subseq using BED (--beb) or GTF (--gtf) file.
  • seqkit locate: add flag -G/--non-greedy, non-greedy mode, faster but may miss motifs overlaping with others.
• SeqKit v0.5.1 - 2017-03-12
  • seqkit restart: fix bug of flag parsing
• SeqKit v0.5.0 - 2017-03-11
  • new command seqkit restart, for resetting start position for circular genome.
  • seqkit sliding: add flag -g/--greedy, exporting last subsequences even shorter than windows size.
  • seqkit seq:
    • add flag -m/--min-len and -M/--max-len to filter sequences by length.
    • rename flag -G/--gap-letter to -G/--gap-letters.
  • seqkit stat:
    • renamed to seqkit stats, don't worry, old name is still available as an alias.
    • add new flag -a/all, for all statistics, including sum_gap, N50, and L50.
• SeqKit v0.4.5 - 2017-02-26
  • seqkit seq: fix bug of failing to reverse quality of FASTQ sequence
• SeqKit v0.4.4 - 2017-02-17
  • seqkit locate: fix bug of missing regular-expression motifs containing non-DNA characters (e.g., ACT.{6,7}CGG) from motif file (-f).
  • compiled with go v1.8.
• SeqKit v0.4.3 - 2016-12-22
  • fix bug of seqkit stat: min_len always be 0 in versions: v0.4.0, v0.4.1, v0.4.2
• SeqKit v0.4.2 - 2016-12-21
  • fix header information of seqkit subseq when restriving up- and down-steam sequences using GTF/BED file.
• SeqKit v0.4.1 - 2016-12-16
  • enchancement: remove redudant regions for seqkit locate.
• SeqKit v0.4.0 - 2016-12-07
  • fix bug of seqkit locate, e.g, only find two locations (1-4, 7-10, missing 4-7) of ACGA in ACGACGACGA.
  • better output of seqkit stat for empty file.
• SeqKit v0.3.9 - 2016-12-04
  • fix bug of region selection for blank sequences. affected commands include seqkit subseq --region, seqkit grep --region, seqkit split --by-region.
  • compile with go1.8beta1.
• SeqKit v0.3.8.1 - 2016-11-25
  • enhancement and bugfix of seqkit common: two or more same files allowed, fix log information of number of extracted sequences in the first file.
• SeqKit v0.3.8 - 2016-12-24
  • enhancement of seqkit common: better handling of files containing replicated sequences
• SeqKit v0.3.7 - 2016-12-23
  • fix bug in seqkit split --by-id when sequence ID contains invalid characters for system path.
  • add more flags validation for seqkit replace.
  • enhancement: raise error when key pattern matches multiple targes in cases of replacing with key-value files and more controls are added.
  • changes: do not wrap sequence and quality in output for FASTQ format.
• SeqKit v0.3.6 - 2016-11-03
  • add new feature for seqkit grep: new flag -R (--region) for specifying sequence region for searching.
• SeqKit v0.3.5 - 2016-10-30
  • fig bug of seqkit grep: flag -i (--ignore-case) did not work when not using regular expression
• SeqKit v0.3.4.1 - 2016-09-21
  • improve performance of reading (~10%) and writing (100%) gzip-compressed file by using github.com/klauspost/pgzip package
  • add citation
• SeqKit v0.3.4 - 2016-09-17
  • bugfix: seq wrongly handles only the first one sequence file when multiple files given
  • new feature: fx2tab can output alphabet letters of a sequence by flag -a (--alphabet)
  • new feature: new flag -K (--keep-key) for replace, when replacing with key-value file, one can choose keeping the key as value or not.
• SeqKit v0.3.3 - 2016-08-18
  • fix bug of seqkit replace, wrongly starting from 2 when using {nr} in -r (--replacement)
  • new feature: seqkit replace supports replacement symbols {nr} (record number) and {kv} (corresponding value of the key ($1) by key-value file)
• SeqKit v0.3.2 - 2016-08-13
  • fix bug of seqkit split, error when target file is in a directory.
  • improve performance of seqkit spliding for big sequences, and output last part even if it's shorter than window sze, output of FASTQ is also supported.
• SeqKit v0.3.1.1 - 2016-08-07
  • compile with go1.7rc5, with higher performance and smaller size of binary file
• SeqKit v0.3.1 - 2016-08-02
  • improve speed of seqkit locate
• SeqKit v0.3.0 - 2016-07-28
  • use fork of github.com/brentp/xopen, using zcat for speedup of .gz file reading on *nix systems.
  • improve speed of parsing sequence ID when creating FASTA index
  • reduce memory usage of seqkit subseq --gtf
  • fix bug of seqkit subseq when using flag --id-ncbi
  • fix bug of seqkit split, outdir error
  • fix bug of seqkit seq -p, last base is wrongly failed to convert when sequence length is odd.
  • add "sum_len" result for output of seqkit stat
• seqkit v0.2.9 - 2016-07-24
  • fix minor bug of seqkit split and seqkit shuffle, header name error due to improper use of pointer
  • add option -O (--out-dir) to seqkit split
• seqkit v0.2.8 - 2016-07-19
  • improve speed of parsing sequence ID, not using regular expression for default --id-regexp
  • improve speed of record outputing for small-size sequences
  • fix minor bug: seqkit seq for blank record
  • update benchmark result
• seqkit v0.2.7 - 2016-07-18
  • reduce memory usage by optimize the outputing of sequences. detail: using BufferedByteSliceWrapper to resuse bytes.Buffer.
  • reduce memory usage and improve speed by using custom buffered reading mechanism, instead of using standard library bufio, which is slow for large genome sequence.
  • discard strategy of "buffer" and "chunk" of FASTA/Q records, just parse records one by one.
  • delete global flags -c (--chunk-size) and -b (--buffer-size).
  • add function testing scripts
• seqkit v0.2.6 - 2016-07-01
  • fix bug of seqkit subseq: Inplace subseq method leaded to wrong result
• seqkit v0.2.5.1
  • fix a bug of seqkit subseq: chromesome name was not be converting to lower case when using --gtf or --bed
• seqkit v0.2.5 - 2016-07-01
  • fix a serious bug brought in v0.2.3, using unsafe method to convert string to []byte
  • add awk-like built-in variable of record number ({NR}) for seqkit replace
• seqkit v0.2.4.1 - 2016-06-12
  • fix several bugs from library bio, affected situations:
    • Locating patterns in sequences by pattern FASTA file: seqkit locate -f
    • Reading FASTQ file with record of which the quality starts with +
  • add command version
• seqkit v0.2.4 - 2016-05-31
  • add subcommand head
• seqkit v0.2.3 - 2016-05-08
  • reduce memory occupation by avoid copy data when convert string to []byte
  • speedup reverse-complement by avoid repeatly calling functions
• seqkit v0.2.2 - 2016-05-06
  • reduce memory occupation of subcommands that use FASTA index
• seqkit v0.2.1 - 2016-05-02
  • improve performance of outputing.
  • fix bug of seqkit seq -g for FASTA fromat
  • some other minor fix of code and docs
  • update benchmark results
• seqkit v0.2.0 - 2016-04-29
  • reduce memory usage of writing output
  • fix bug of subseq, shuffle, sort when reading from stdin
  • reduce memory usage of faidx
  • make validating sequences an optional option in seq command, it saves some time.
• seqkit v0.1.9 - 2016-04-26
  • using custom FASTA index file extension: .seqkit.fai
  • reducing memory usage of sample --number --two-pass
  • change default CPU number to 2 for multi-cpus computer, and 1 for single-CPU computer
• seqkit v0.1.8 - 2016-04-24
  • add subcommand rename to rename duplicated IDs
  • add subcommand faidx to create FASTA index file
  • utilize faidx to improve performance of subseq
  • shuffle, sort and split support two-pass mode (by flag -2) with faidx to reduce memory usage.
  • document update
• seqkit v0.1.7 - 2016-04-21
  • add support for (multi-line) FASTQ format
  • update document, add technical details
  • rename subcommands fa2tab and tab2fa to fx2tab and tab2fx
  • add subcommand fq2fa
  • add column "seq_format" to stat
  • add global flag -b (--bufer-size)
  • little change of flag in subseq and some other commands
• seqkit v0.1.6 - 2016-04-07
  • add subcommand replace
• seqkit v0.1.5.2 - 2016-04-06
  • fix bug of grep, when not using flag -r, flag -i will not take effect.
• seqkit v0.1.5.1
  • fix result of seqkit sample -n
  • fix benchmark script
• seqkit v0.1.5 - 2016-03-29
  • add global flag --id-ncbi
  • add flag -d (--dup-seqs-file) and -D (--dup-num-file) for subcommand rmdup
  • make using MD5 as an optional flag -m (--md5) in subcommand rmdup and common
  • fix file name suffix of seqkit split result
  • minor modification of sliding output
• seqkit v0.1.4.1 - 2016-03-27
  • change alignment of stat output
  • preciser CPUs number control
• seqkit v0.1.4 - 2016-03-25
  • add subcommand sort
  • improve subcommand subseq: supporting of getting subsequences by GTF and BED files
  • change name format of sliding result
  • prettier output of stat
• seqkit v0.1.3.1 - 2016-03-16
  • Performance improvement by reducing time of cleaning spaces
  • Document update
• seqkit v0.1.3 - 2016-03-15
  • Further performance improvement
  • Rename sub command extract to grep
  • Change default value of flag --threads back CPU number of current device, change default value of flag --chunk-size back 10000 sequences.
  • Update benchmark
• seqkit v0.1.2 - 2016-03-14
  • Add flag --dna2rna and --rna2dna to subcommand seq.
• seqkit v0.1.1 - 2016-03-13
  • 5.5X speedup of FASTA file parsing by avoid using regular expression to remove spaces (detail ) and using slice indexing instead of map to validate letters (detail)
  • Change default value of global flag -- thread to 1. Since most of the subcommands are I/O intensive, For computation intensive jobs, like extract and locate, you may set a bigger value.
  • Change default value of global flag --chunk-size to 100.
  • Add subcommand stat
  • Fix bug of failing to automatically detect alphabet when only one record in file.
• seqkit v0.1 - 2016-03-11
  • first release of seqkit