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seqkit
seqkit is a fast, streaming toolkit for fastx files (FASTA or FASTQ). It has 39 subcommands covering nearly every routine sequence-file operation. Before writing a script that reads a fastx file, check the routing table below.
Requires seqkit on $PATH. If it is not there, this skill does not apply — fall back to scripting.
Rules
- Write long flags. Short flags mean different things in different
subcommands: -s is --by-seq in rmdup but --rand-seed in sample, --step in sliding, and --pattern in mutate. -p is --pattern in grep but --point in mutate. Long flags are unambiguous and self-documenting. See references/traps.md for the collision table, needed when reading someone else's command.
- `seqkit <cmd> --help` is the authority on whether a flag exists. Never
assume a flag from another subcommand transfers. This document does not list flags on purpose — --help cannot go stale, and published seqkit docs demonstrably do.
- If it isn't fastx, it isn't seqkit. Interval arithmetic, BAM
manipulation, alignment, and tabular wrangling are other tools' jobs. See references/boundaries.md.
Leave global flags (-j/--threads, -w/--line-width, --id-regexp) at their defaults unless the user asks.
Routing table
⚠ marks a subcommand with a documented trap — read its entry in references/traps.md before using it.
Inspect and summarise
| Want to... | Command |
|---|---|
| Count records, total bases, min/max/mean length, GC%, Q20/Q30 | seqkit stats ⚠ (lengths and GC include gaps) |
| Get N50, L50, or any Nx | seqkit stats --all --tabular -N 50,90 ⚠ |
| Get machine-readable stats for downstream processing | seqkit stats --tabular ⚠ |
| Get per-record length, GC, name, or average quality as a table | seqkit fx2tab ⚠ |
| Find records containing ambiguous or unexpected bases | seqkit fx2tab --alphabet ⚠ |
| Get a per-sequence MD5 hash | seqkit fx2tab --seq-hash ⚠ |
| Tabulate several files at once, tagging each row with its source file (2.14+) | seqkit fx2tab --file-name ⚠ |
| Prove two files contain the same sequences, any order or strand | seqkit sum ⚠ |
| Prove two files contain the same records, IDs included (2.14+) | seqkit sum --include-id ⚠ |
| Watch length/quality/GC distributions while a pipeline runs | seqkit watch |
| Get BAM record statistics or histograms | seqkit bam |
Filter and subset
| Want to... | Command |
|---|---|
| Keep sequences above/below a length | seqkit seq --min-len / --max-len ⚠ |
| Keep reads above an average quality | seqkit seq --min-qual ⚠ |
| Filter and transform in one pass (2.13+) | seqkit seq --f-pattern ⚠ |
| Pull out records by ID, from a list | seqkit grep --pattern-file ⚠ (matches the whole ID; use --use-regexp for partial) |
| Pull out records by ID, preserving the list's order | seqkit faidx --region-file ⚠ |
| Take the first N records | seqkit head |
| Take the first N bases' worth of records | seqkit head --length 2G |
| Take records 101-200, or the last 100 | seqkit range --range |
| Take a random subset | seqkit sample2 (2.13+) ⚠ |
| Extract a region by coordinates | seqkit subseq --region ⚠ |
| Extract regions listed in a BED or GTF file | seqkit subseq --bed / --gtf ⚠ |
| Extract features plus flanking sequence | seqkit subseq --gtf --up-stream ⚠ |
| Extract a named region from an indexed FASTA | seqkit faidx ⚠ |
| Pull out the first genome from a multi-strain file by name prefix | seqkit head-genome |
Search
| Want to... | Command |
|---|---|
| Find records whose ID matches a pattern | seqkit grep --use-regexp ⚠ |
| Find records containing a subsequence or motif | seqkit grep --by-seq ⚠ |
| Find records containing a motif, allowing mismatches | seqkit grep --by-seq --max-mismatch ⚠ |
| Search with IUPAC/degenerate bases | seqkit grep --by-seq --degenerate ⚠ |
| Get the coordinates of every motif match | seqkit locate ⚠ |
| Get motif matches as BED or GTF | seqkit locate --bed / --gtf ⚠ |
| Scan for restriction sites from a FASTA of motifs | seqkit locate --degenerate --pattern-file ⚠ |
| Do in-silico PCR from a primer pair | seqkit amplicon ⚠ |
| Locally align short queries into long sequences | seqkit fish ⚠ |
Convert and tabulate
| Want to... | Command |
|---|---|
| Convert FASTQ to FASTA | seqkit fq2fa |
| Recover FASTQ (with qualities) for sequences you only have as FASTA | seqkit fa2fq |
| Turn fastx into a TSV for downstream tools | seqkit fx2tab ⚠ |
| Turn a TSV back into fastx | seqkit tab2fx |
| Convert FASTQ quality encoding (Solexa/Illumina/Sanger) | seqkit convert |
| Translate DNA/RNA to protein, any genetic code, any frame | seqkit translate |
| Reverse complement | seqkit seq --reverse --complement ⚠ |
| Strip gaps from an alignment | seqkit seq --remove-gaps ⚠ |
| Unwrap FASTA to one line per sequence | seqkit seq --line-width 0 ⚠ |
| Extract just the IDs or just the sequences | seqkit seq --name --only-id / --seq ⚠ |
Set operations and deduplication
| Want to... | Command |
|---|---|
| Remove duplicate records by ID or by sequence | seqkit rmdup ⚠ (--by-seq also collapses reverse complements) |
| Get a report of which records were duplicated | seqkit rmdup --dup-num-file ⚠ |
| Find sequences shared across several files | seqkit common ⚠ |
| Re-pair paired-end reads, dropping or saving singletons | seqkit pair ⚠ |
| Join sequences with the same ID across files | seqkit concat ⚠ |
| Repeat each record N times | seqkit duplicate |
Split and sample
| Want to... | Command |
|---|---|
| Split into N files, or files of N records | seqkit split2 --by-part / --by-size ⚠ |
| Split into one file per record, named by ID | seqkit split2 --by-size 1 --seqid-as-filename ⚠ |
| Split by ID, by a regex on the header, or by region | seqkit split ⚠ |
| Split paired-end FASTQ, keeping pairs together | seqkit split2 --read1 --read2 ⚠ |
| Take a random sample of records | seqkit sample2 (2.13+) ⚠ |
| Chop a sequence into fixed-size windows | seqkit sliding |
| Merge sliding windows back into intervals | seqkit merge-slides |
Edit and reorder
| Want to... | Command |
|---|---|
| Rewrite headers with a regex | seqkit replace ⚠ |
| Substitute, mask, or delete bases by regex (FASTQ from 2.14+) | seqkit replace --by-seq ⚠ |
| Rewrite headers from a TSV lookup table | seqkit replace --kv-file ⚠ |
| Number records sequentially, or stamp the filename into the header | seqkit replace with {nr} / {fbne} ⚠ |
| Make duplicate IDs unique | seqkit rename ⚠ |
| Introduce point mutations, insertions, or deletions | seqkit mutate ⚠ |
| Rotate a circular genome to a new origin | seqkit restart |
| Sort by ID, length, or sequence | seqkit sort ⚠ |
| Shuffle record order | seqkit shuffle ⚠ |
Streaming and repair
| Want to... | Command |
|---|---|
| Repair a truncated or malformed FASTQ, skipping bad records | seqkit sana |
| Stream fastx files as they appear in a directory | seqkit scat |
| Feed a long list of input files | any command, with --infile-list |
References
- references/traps.md — behaviours that produce plausible
but wrong output, or exhaust memory. Indexed by subcommand.
- references/recipes.md — multi-command compositions
where the composition is the insight.
- references/boundaries.md — what seqkit does not do,
and what does it instead.
Verified against seqkit v2.14.0. If a command here is unknown to your seqkit, it is older — check seqkit version.