fastqc-rs

A fast quality control tool for FASTQ files written in rust inspired by fastQC. Results are written to stdout as a self containing html report with visualizations for all statistics. Summary files for usage with MultiQC can also be generated.

Available statistics are:

• Read length
• Sequence quality score
• Sequence quality per base
• Sequence content per base
• k-mer content
• GC content

For a detailed list of changes, take a look at the CHANGELOG.

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