taf-seqkit

taf-seqkit packages SeqKit 2.13.0-r2, an ultrafast toolkit for FASTA/Q sequence manipulation and lightweight BAM monitoring.

Package identity:

• name: seqkit
• command: taf-seqkit
• kind: tool
• TAFFISH version: 2.13.0-r2
• container image: ghcr.io/taffish/seqkit:2.13.0-r2
• upstream release: v2.13.0
• runtime version string: seqkit v2.13.0
• upstream license: MIT
• Linux amd64 archive SHA256: 7d686de448464fada1b1988e2e07d693bec68768312da62846bc0e2b502bfc46
• Linux arm64 archive SHA256: 2bce55ea352ceab56a428b2d6e06e6565485a446c17dc17cadb5dc28ab7a9cdc

What Is Included

This app installs the official upstream static Linux binary for the target container architecture. SeqKit itself is a single executable and does not require external aligners, databases, models, or interpreters.

SeqKit supports common FASTA/Q work including:

• statistics with stats
• sequence transformation with seq
• format conversion with fq2fa, fx2tab, and tab2fx
• search and motif location with grep and locate
• subsequence extraction with subseq and faidx
• set operations with sample, sample2, rmdup, and common
• splitting and ordering with split, split2, sort, and shuffle
• editing with replace, rename, concat, restart, and mutate
• translation with translate
• sequence checksums with sum
• lightweight BAM monitoring with bam

SeqKit reads and writes common compressed formats itself, including gzip, xz, zstd, bzip2, and LZ4 where supported by upstream SeqKit.

Command Mode

taf-seqkit --help prints this TAFFISH app help. Use -- only when passing option-leading arguments to the default upstream command:

taf-seqkit -- --help

SeqKit is a subcommand-based CLI. Because this TAFFISH app keeps command_mode = true, use the upstream executable name when running SeqKit subcommands:

taf-seqkit seqkit version
taf-seqkit seqkit stats reads.fa reads.fq.gz
taf-seqkit seqkit fq2fa reads.fq.gz > reads.fa
taf-seqkit seqkit grep -p chrM genome.fa

Avoid ambiguous forms such as taf-seqkit stats reads.fa; TAFFISH may treat stats as a container command rather than as seqkit stats.

Common Workflows

Compute FASTA/FASTQ statistics:

taf-seqkit seqkit stats *.fa *.fq.gz

Convert FASTQ to FASTA:

taf-seqkit seqkit fq2fa reads.fq.gz > reads.fa

Filter by sequence length:

taf-seqkit seqkit seq -m 100 -M 10000 contigs.fa > contigs.100-10000.fa

Extract selected records:

taf-seqkit seqkit grep -f ids.txt sequences.fa > selected.fa

Extract FASTA intervals:

taf-seqkit seqkit faidx genome.fa chr1:1000-2000 > chr1.1000-2000.fa

Locate sequence motifs:

taf-seqkit seqkit locate -p ACGT genome.fa > motifs.tsv

Write LZ4-compressed output:

taf-seqkit seqkit seq -o sequences.fa.lz4 sequences.fa

Boundaries

This app exposes the upstream SeqKit executable and its built-in subcommands. It does not bundle external tools such as Samtools, aligners, genome databases, shell completion installation, or tutorial datasets.

The bam subcommand is included because it is part of SeqKit, but this app does not turn SeqKit into a full BAM/SAM toolchain. Use dedicated TAFFISH apps such as Samtools for sorting, indexing, conversion, or alignment-centric workflows.

The smoke tests verify representative FASTA, FASTQ, subcommand, LZ4 compression, and version paths. They do not exhaustively test every SeqKit subcommand or every compression format.

Platform

The image uses official upstream static Linux binaries and is intended for native linux/amd64 and linux/arm64 container platforms.

License Boundary

The TAFFISH app packaging files are licensed under Apache-2.0. The packaged upstream SeqKit software is covered by: MIT. Bundled third-party components, datasets, models, and external resources keep their own license terms.

Upstream

• Upstream repository: https://github.com/shenwei356/seqkit
• Upstream documentation: https://bioinf.shenwei.me/seqkit/
• Upstream release: https://github.com/shenwei356/seqkit/releases/tag/v2.13.0
• Upstream license: MIT

Primary citation:

• Shen W, Sipos B, Zhao L. 2024. SeqKit2: A Swiss Army Knife for Sequence and Alignment Processing. iMeta e191. DOI: 10.1002/imt2.191.
• Shen W et al. 2016. SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS ONE. DOI: 10.1371/journal.pone.0163962, PMID: 27706213.