LightQC is a lightweight Nanopore/PacBio reads quality control tool that relies on FASTQ files to evaluate the quality of one dataset or compare multiple datasets.
LightQC computes some metrics from the reads file such as PHRED score and reads length as well as from the alignment of the reads against a reference genome.
This software only depends on Python 3 with some additional packages.
- Install the dependencies with pip.
pip install pandas, numpy, scipy, plotly, ipykernel
-
Install Minimap2 as described in Minimap2 Installation. Minimap2 must be available on the PATH for LightQC.
-
Download this script and add the script location to the path or move the script to a localization in your path (such as $HOME/bin).
git clone https://github.com/drs/LightQC
Typical usage :
LightQC -g genome.fasta -r reads.fastq -x nanopore -o Output/
LightQC is still in development. Feel free to submit any feature request through the GitHub Issues tracker.
While this tools aims at providing a fast and lightweight all-in-one solution for Nanopore/PacBio reads quality control, alternatives tools offer different interesting features :