Seqkit

seqkit

Quick Start

• Command: seqkit <subcommand> [options] <input>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/seqkit
• Version: 2.13.0
• Full reference: See references/help.md for complete subcommand options

When To Use This Tool

• General-purpose FASTA/FASTQ inspection, filtering, conversion, and manipulation.
• Quick sequence operations without writing custom scripts.
• Use it when you need one clean subcommand instead of an ad hoc awk or Python one-liner.
• Especially useful for stats, grep-like selection, subsequences, and format conversion.

Common Patterns

# 1) Basic FASTQ summary statistics
seqkit stats reads.fastq.gz

# 2) Filter sequences by minimum length and keep only IDs
seqkit seq -m 200 input.fa.gz

# 3) Search by ID or pattern
seqkit grep -p TP53 proteins.fa.gz

# 4) Convert FASTA/Q to tabular form
seqkit fx2tab reads.fastq.gz

# 5) Remove duplicates
seqkit rmdup input.fa.gz -o dedup.fa.gz

Recommended Workflow

1. Start with seqkit stats to understand the file you are about to manipulate.
2. Choose the narrowest subcommand that matches the operation instead of overloading shell text processing.
3. Keep outputs compressed when appropriate; SeqKit handles compressed I/O directly.
4. Use subcommand-specific help for anything beyond the common workflows.

Guardrails

• seqkit version is the version command; seqkit --version is not the right interface here.
• Use seqkit <subcommand> --help for real usage details, because the top-level command is just a dispatcher.
• Output compression is handled automatically from the filename suffix.
• SeqKit can parse IDs with its own regex rules, so be explicit if FASTA headers use unusual formats.