#fastq #quality #control #sequence #tool #content #statistics

app fastqc-rs

A fast quality control tool for FASTQ files written in rust

9 releases

0.3.4 Aug 8, 2024
0.3.2 Jun 6, 2022
0.3.1 Jan 26, 2022
0.3.0 Nov 19, 2021
0.1.1 Feb 14, 2021

#126 in Science

MIT license

605KB
550 lines

fastqc-rs logo fastqc-rs

Rust Crates.io Crates.io Crates.io install with bioconda Bioconda downloads

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

Dependencies

~26–36MB
~633K SLoC