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

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)

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

W Shen, S Le, Y Li*, F Hu*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLOS ONE. doi:10.1371/journal.pone.0163962.

Contributors

Acknowledgements

We thank Lei Zhang for testing SeqKit, and also thank Jim Hester, author of fasta_utilities, for advice on early performance improvements of for FASTA parsing and Brian Bushnell, author of BBMaps, for advice on naming SeqKit and adding accuracy evaluation in benchmarks. We also thank Nicholas C. Wu from the Scripps Research Institute, USA for commenting on the manuscript and Guangchuang Yu from State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, HK for advice on the manuscript.

We thank Li Peng for reporting many bugs.

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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