SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation

• Documents: http://bioinf.shenwei.me/seqkit (Usage, FAQs, Tutorial, and Benchmark)
• Source code: https://github.com/shenwei356/seqkit
• Latest version:
• Please cite: ,
• Others:

Features

• Easy to install (download)
  • Providing statically linked executable binaries for multiple platforms (Linux/Windows/macOS, amd64/arm64)
  • Light weight and out-of-the-box, no dependencies, no compilation, no configuration
  • conda install -c bioconda seqkit
• Easy to use
  • Ultrafast (see technical-details and benchmark)
  • Seamlessly parsing both FASTA and FASTQ formats
  • Supporting (gzip/xz/zstd/bzip2 compressed) STDIN/STDOUT and input/output file, easily integrated in pipe
  • Reproducible results (configurable rand seed in sample and shuffle)
  • Supporting custom sequence ID via regular expression
  • Supporting Bash/Zsh autocompletion
• Versatile commands (usages and examples)
  • Practical functions supported by 38 subcommands

Installation

Go to Download Page for more download options and changelogs, or install via conda:

conda install -c bioconda seqkit

Subcommands

Category	Command	Function	Input	Strand-sensitivity	Multi-threads
Basic operation	seq	Transform sequences: extract ID/seq, filter by length/quality, remove gaps…	FASTA/Q
	stats	Simple statistics: #seqs, min/max_len, N50, Q20%, Q30%…	FASTA/Q		✓
	subseq	Get subsequences by region/gtf/bed, including flanking sequences	FASTA/Q	+ or/and -
	sliding	Extract subsequences in sliding windows	FASTA/Q	+ only
	faidx	Create the FASTA index file and extract subsequences (with more features than samtools faidx)	FASTA	+ or/and -
	translate	translate DNA/RNA to protein sequence	FASTA/Q	+ or/and -
	watch	Monitoring and online histograms of sequence features	FASTA/Q
	scat	Real time concatenation and streaming of fastx files	FASTA/Q		✓
Format conversion	fq2fa	Convert FASTQ to FASTA format	FASTQ
	fx2tab	Convert FASTA/Q to tabular format	FASTA/Q
	fa2fq	Retrieve corresponding FASTQ records by a FASTA file	FASTA/Q	+ only
	tab2fx	Convert tabular format to FASTA/Q format	TSV
	convert	Convert FASTQ quality encoding between Sanger, Solexa and Illumina	FASTA/Q
Searching	grep	Search sequences by ID/name/sequence/sequence motifs, mismatch allowed	FASTA/Q	+ and -	partly, -m
	locate	Locate subsequences/motifs, mismatch allowed	FASTA/Q	+ and -	partly, -m
	amplicon	Extract amplicon (or specific region around it), mismatch allowed	FASTA/Q	+ and -	partly, -m
	fish	Look for short sequences in larger sequences	FASTA/Q	+ and -
Set operation	sample	Sample sequences by number or proportion	FASTA/Q
	rmdup	Remove duplicated sequences by ID/name/sequence	FASTA/Q	+ and -
	common	Find common sequences of multiple files by id/name/sequence	FASTA/Q	+ and -
	duplicate	Duplicate sequences N times	FASTA/Q
	split	Split sequences into files by id/seq region/size/parts (mainly for FASTA)	FASTA preffered
	split2	Split sequences into files by size/parts (FASTA, PE/SE FASTQ)	FASTA/Q
	head	Print first N FASTA/Q records	FASTA/Q
	head-genome	Print sequences of the first genome with common prefixes in name	FASTA/Q
	range	Print FASTA/Q records in a range (start:end)	FASTA/Q
	pair	Patch up paired-end reads from two fastq files	FASTA/Q
Edit	replace	Replace name/sequence by regular expression	FASTA/Q	+ only
	rename	Rename duplicated IDs	FASTA/Q
	concat	Concatenate sequences with same ID from multiple files	FASTA/Q	+ only
	restart	Reset start position for circular genome	FASTA/Q	+ only
	mutate	Edit sequence (point mutation, insertion, deletion)	FASTA/Q	+ only
	sana	Sanitize broken single line FASTQ files	FASTQ
Ordering	sort	Sort sequences by id/name/sequence/length	FASTA preffered
	shuffle	Shuffle sequences	FASTA preffered
BAM processing	bam	Monitoring and online histograms of BAM record features	BAM
Miscellaneous	sum	Compute message digest for all sequences in FASTA/Q files	FASTA/Q		✓
	merge-slides	Merge sliding windows generated from seqkit sliding	TSV

Notes:

• Strand-sensitivity:
  • + only: only processing on the positive/forward strand.
  • + and -: searching on both strands.
  • + or/and -: depends on users' flags/options/arguments.
• Multiple-threads: Using the default 4 threads is fast enough for most commands, some commands can benefit from extra threads.

Citation

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.

Contributors

• Wei Shen
• Botond Sipos: bam, scat, fish, sana, watch.
• others

Acknowledgements

We thank all users for their valuable feedback and suggestions. We thank all contributors for improving the code and documentation.

We appreciate Klaus Post for his fantastic packages ( compress and pgzip ) which accelerate gzip file reading and writing.

Contact

Create an issue to report bugs, propose new functions or ask for help.

License

MIT License

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