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

Try SeqKit in your browser (Tutorials and Exercises provided by sandbox.bio)
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/lz4 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

Method 1: Download binaries

Go to Download Page, where you can find download links to various platforms.

Method 2: Install via Pixi

pixi global install -c bioconda seqkit

Method 3: Install via conda

conda install -c bioconda seqkit

Method 4: Install via homebrew

brew install 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/maxlen, 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 | | | | |sample2 |Sample sequences by number or proportion (version 2) |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 the first N FASTA/Q records, or leading records whose total length >= L |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 (rotate) for circular genomes |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

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.