seqkit
seqkit is a cross-platform toolkit for FASTA/FASTQ file manipulation. Liatir uses the stats subcommand to compute sequence statistics — read/sequence counts, length distribution, GC content, N50, and quality rates.
Details
| Property | Value |
|---|---|
| Type | Native tool |
| Binary | seqkit |
| Subcommand | stats |
Installation
Nothing to install. This tool ships inside Liatir and runs at the version this release was tested with; it updates when Liatir updates. The tool page shows Included with Liatir and the version it is running.
On Windows it runs through WSL2 — see Windows and WSL2.
Accepted inputs
| Extension | Description |
|---|---|
.fasta, .fa, .fna | Uncompressed FASTA |
.fasta.gz, .fa.gz | Gzip-compressed FASTA |
.fastq, .fq | Uncompressed FASTQ |
.fastq.gz, .fq.gz | Gzip-compressed FASTQ |
seqkit reads both compressed and uncompressed files directly — no need to decompress them first.
Running seqkit stats
- Navigate to Tools → seqkit.
- Select a FASTA or FASTQ file from your Data library.
- Optionally enable extended stats to include N50, Q20, Q30, and GC content (adds a small overhead for large files).
- Click Run stats.
Output metrics
Basic stats (always included)
| Metric | Description |
|---|---|
| Sequences | Total number of sequences (reads for FASTQ, entries for FASTA) |
| Total length | Sum of all sequence lengths |
| Min length | Shortest sequence |
| Avg length | Mean sequence length |
| Max length | Longest sequence |
Extended stats (-a flag)
| Metric | Description |
|---|---|
| N50 | Half of total assembly length is contained in sequences ≥ N50. Primary assembly quality metric. |
| GC content | Percentage of guanine + cytosine bases |
| Q20 rate | Fraction of bases with Phred quality ≥ 20 (FASTQ only) |
| Q30 rate | Fraction of bases with Phred quality ≥ 30 (FASTQ only) |
N50 for assemblies
N50 is a key metric for genome assemblies. A higher N50 means larger contigs. For chromosome-level assemblies N50 ≈ chromosome length; for fragmented assemblies N50 may be a few hundred Kb. A low N50 in a FASTA intended to be a complete genome suggests the assembly is highly fragmented.