Get sequence statistics for FASTA/FASTQ with seqkit
Use seqkit stats to print read and contig counts, length distribution, N50, GC, and quality metrics for any FASTA or FASTQ file.
Prerequisites
- seqkit installed (`conda install -c bioconda seqkit`)
- A FASTA or FASTQ file (optionally gzipped)
1Print basic stats for a FASTQ
Point seqkit stats at your file to get the read count, total bases, and length range. It reads gzipped input directly, so there is no need to decompress first.
seqkit stats reads.fastq.gzExpected output
file format type num_seqs sum_len min_len avg_len max_len
reads.fastq.gz FASTQ DNA 1,000,000 151,000,000 151 151.0 1512Get N50, GC, and quality with -a
Add the -a (all statistics) flag to compute N50, GC content, and Q20/Q30 percentages. This is what you want when assessing an assembly or a reference genome; quality columns read 0 for FASTA since it carries no base qualities.
seqkit stats -a genome.fastaExpected output
file format type num_seqs sum_len min_len avg_len max_len Q1 Q2 Q3 sum_gap N50 Q20(%) Q30(%) GC(%)
genome.fasta FASTA DNA 215 128,451,203 512 597,447.5 9,215,872 8,412 45,120 215,304 0 4,215,304 0.00 0.00 41.20Troubleshooting
seqkit: command not found
Install it from Bioconda: `conda install -c bioconda seqkit`.
You only see basic columns and need N50 or GC
Add the `-a` (all statistics) flag. To summarize many files in one table, run `seqkit stats -a *.fasta`.