fastqc-rs
| Crates.io | fastqc-rs |
| lib.rs | fastqc-rs |
| version | 0.3.4 |
| created_at | 2021-02-11 16:05:47.162486+00 |
| updated_at | 2024-08-08 07:21:19.885728+00 |
| description | A fast quality control tool for FASTQ files written in rust |
| homepage | https://fastqc-rs.github.io |
| repository | https://github.com/fastqc-rs/fastqc-rs |
| max_upload_size | |
| id | 353836 |
| size | 1,630,310 |
Felix Wiegand (fxwiegand)
documentation
README
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 |