fastqc-rs

A fast quality control tool for FASTQ files written in rust inspired by fastQC.

Available statistics are: - Read length - Sequence quality score - Sequence quality per base - Sequence content per base - k-mer content - GC content

Installation

There are multiple ways to install fastqc-rs:

Bioconda

fastqc-rs is available via Bioconda. With Bioconda set up, installation is as easy as

conda install fastqc-rs

Cargo

If the Rust compiler and associated Cargo are installed, fastqc-rs can be installed via

cargo install fastqc-rs

Source

Download the source code and within the root directory of source run

cargo install

Usage

fqc -q path/to/my_sequence.fastq > report.html

Arguments:

| Parameter | Default | Description |
| :------------------------ |:-------------:| :-------------| | -q --fastq | - |The path to the FASTQ file to use | -k | 5 |The length k of k-mers for k-mer counting | -s --summary | - |Creates an output file for usage with MultiQC under the given path