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

Subcommands of SeqKit2

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

  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

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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