count-fasta-rs

Install v0.7.0

Published on Jul 17 2025 at 23:11 UTC

count-fasta-rs

This utility gives some stats on assembly reports

Usage: count-fasta-rs [OPTIONS] [FASTA FILE (.fa .fasta .fna .zip .gz)]...

Arguments:
  [FASTA FILE (.fa .fasta .fna .zip .gz)]...  

Options:
  -c, --csv <CSV>              
  -d, --directory <DIRECTORY>  
  -h, --help                   Print help
  -V, --version                Print version

Installation

Install the binary for your OS and architecture from the latest release page , or use the standalone installers.

Or you can build from source with cargo.

git clone https://github.com/jovillarrealm/count-fasta-rs
cd count-fasta-rs
cargo install --path .

Usage

When a csv file is not specified

count-fasta-rs ../cnsg-scripts/GENOMIC/GCA_024699835_Aphelenchoides-besseyi_AORJ.fna

Output to stdout will look like this

    Total length of sequence:       46759715 bp
    Total number of sequences:      32
    Average contig length is:       1461241 bp
    Largest contig:         18100598 bp
    Shortest contig:                214 bp
    N25 stats:                      25% of total sequence length is contained in the 1 sequences >= 18100598 bp
    N50 stats:                      50% of total sequence length is contained in the 2 sequences >= 16068654 bp
    N75 stats:                      75% of total sequence length is contained in the 3 sequences >= 10965501 bp
    Total GC count:                 19534458 bp
    GC %:                           41.78 %
    Number of Ns:                   2900
    Ns %:                           0.01 %

If the csv file was specified, then the created file will look like this

    filename;assembly_length;number_of_sequences;average_length;largest_contig;shortest_contig;N50;GC_percentage;total_N;N_percentage
    "GCA_024699835_Aphelenchoides-besseyi_AORJ.fna";46759715;32;1461241.09;18100598;214;16068654;41.78;2900;0.01

[!IMPORTANT] If you are setting a -d directory, you should probably set a -c csv file to go with it

Implementation deets

It uses dist as a distribution tool for installation.

[!IMPORTANT] To modify the installation path, it requires to modify install-path in dist-workspace.toml, and run ci again. install-path = "CARGO_HOME"

[!NOTE] Known Bug: .gz files that were compressed with bgzip are read incorrectly.