README.md

fatcat

FASTQ cat

A paged, pretty printer for FASTQ files.

Like zcat reads.fastq.gz | less but nicer.

Kind of a gimmick, mildly useful.

Installation

Cargo:

Requires cargo

cargo install fatcat

Build from source:

Install rust toolchain:

To install please refer to the rust documentation: docs

Clone the repository:

git clone https://github.com/Sam-Sims/fatcat

Build and add to path:

cd fatcat
cargo build --release
export PATH=$PATH:$(pwd)/target/release

All executables will be in the directory fatcat/target/release.

Usage

Basic usage:

fatcat <fastq_file> [options]

Reads will be displayed in a paged format. Use the arrow keys (the scroll wheel and PgUp&PgDown work too) to navigate and q to quit. Read names will be highlighted based on pass/fail of the filters. Green if all filters pass, red if any fail.

Options:

Quality

-q, --quality <min_quality_score>

This will set the threshold for the average quality score of a read. If the average quality score of a read is below this threshold, the Q score will be highlighted in red, and the filter fail.

Length

-l, --length <min_length>

This will set the threshold for the read length. If the read length is below this threshold, the length will be highlighted in red, and the filter fail.

Read descriptions

--show-desc

This will show the read descriptions alongside the read names. Default is to hide them.