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

seqkit must be installed and available in your system PATH.

macOS (Homebrew)

brew install seqkit

conda

conda install -c bioconda seqkit

Ubuntu/Debian

sudo apt install seqkit

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 handles both compressed and uncompressed formats natively without piping through gunzip first.

Running seqkit stats

1. Navigate to Tools → seqkit.
2. Select a FASTA or FASTQ file from your Data library.
3. Optionally enable extended stats to include N50, Q20, Q30, and GC content (adds a small overhead for large files).
4. 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.