A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
See the code
conda install -c bioconda seqkitgzip/xz/zstd/bzip2/lz4 compressed) STDIN/STDOUT and input/output file, easily integrated in pipesample and shuffle)Go to Download Page, where you can find download links to various platforms.
pixi global install -c bioconda seqkit
conda install -c bioconda seqkit
brew install seqkit
| 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 | ||
| 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 preferred | |||
| 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 preferred | ||
| shuffle | Shuffle sequences | FASTA preferred | |||
| 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:
+ only: only processing on the positive/forward strand.+ and -: searching on both strands.+ or/and -: depends on users' flags/options/arguments.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.
bam, scat, fish, sana, watch.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.
Create an issue to report bugs, propose new functions or ask for help.
Overall
Maintained
Code review
Go module
Latest release
Releases this year
64 followers · starred Sep 2026
346 followers · starred Oct 2025
27 followers · starred Nov 2022
54 followers · starred Mar 2022
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
See the code
conda install -c bioconda seqkitgzip/xz/zstd/bzip2/lz4 compressed) STDIN/STDOUT and input/output file, easily integrated in pipesample and shuffle)Go to Download Page, where you can find download links to various platforms.
pixi global install -c bioconda seqkit
conda install -c bioconda seqkit
brew install seqkit
| 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 | ||
| 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 preferred | |||
| 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 preferred | ||
| shuffle | Shuffle sequences | FASTA preferred | |||
| 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:
+ only: only processing on the positive/forward strand.+ and -: searching on both strands.+ or/and -: depends on users' flags/options/arguments.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.
bam, scat, fish, sana, watch.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.
Create an issue to report bugs, propose new functions or ask for help.
Overall
Maintained
Code review
Go module
Latest release
Releases this year
64 followers · starred Sep 2026
346 followers · starred Oct 2025
27 followers · starred Nov 2022
54 followers · starred Mar 2022