Fastoche is a tool designed to effortlessly extract common metrics from Fasta or Fastq files, gzipped or not.
The only dependency to build the code from source is the Rust compiler.
git clone https://github.com/institut-de-genomique/fastoche
cd fastoche
cargo install --path . --root .If everything went as expected, the fastoche binary file will be in the bin folder.
You can run fastoche -h to get a detailed view of fastoche options. The basic usage would be to give some fasta/fastq files and rename the columns to get customized table headers:
fastoche -f reads.fastq.gz -f ../assembly.fasta -r "Reads,Assembly"
┌──────────────┬────────────────────┬──────────────────────┐
│ │ Reads │ Assembly │
├──────────────┼────────────────────┼──────────────────────┤
│ Cumul. size │ 5,957,360 │ 2,275,546,859 │
│ Seq. number │ 1,000 │ 33,632 │
│ N50 (L50) │ 8,383 (229) │ 119,535 (5,017) │
│ N80 (L80) │ 4,170 (530) │ 43,439 (14,548) │
│ N90 (L90) │ 3,016 (697) │ 27,849 (21,103) │
│ Min. size │ 159 │ 3,489 │
│ Max. size │ 28,705 │ 1,362,978 │
│ Avg. size │ 5,957 │ 67,660 │
│ auN │ 9,598 │ 176,634 │
│ Ns Number │ 0 (0.00%) │ 0 (0.00%) │
│ GC Number │ 2,542,770 (42.68%) │ 995,607,282 (43.75%) │
│ Mean quality │ 9 │ 0 │
└──────────────┴────────────────────┴──────────────────────┘
The -f flag can be given as many times as needed and can contain a mix of fasta and fastq files. The Mean quality row is shown only for Fastq files and is always equal to 0 for Fasta files, as Phred qualities are not available.