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 |
#128 in Science
605KB
550 lines
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 |
Dependencies
~28–39MB
~665K SLoC