Detect interesting SARS-CoV-2 spike protein variants from Sanger sequencing data.
Project description
Detect interesting SARS-CoV-2 spike protein variants from Sanger sequencing data
covid-spike-classification
is a script to call interesting SARS-CoV-2 spike protein variants
from Sanger sequencing to support the Danish COVID-19 monitoring efforts.
Using Sanger-sequenced RT-PCR product of the spike protein, this tool should pick up all relevant mutations currently tracked and give a table with one row per sample and a yes/no/failed column per tracked mutation.
This workflow is built and maintained at https://github.com/kblin/covid-spike-classification
Installation
For now, covid-spike-classification
is distributed via this git repository.
covid-spike-classification
depends on three excellent tools to do most of the work:
- tracy (version 0.5.3 tested)
- bowtie2 (version 2.4.2 tested)
- samtools (version 1.11 tested)
If you have conda
installed, the easiest way to get started is to just install these via calling
git clone https://github.com/kblin/covid-spike-classification.git
cd covid-spike-classification
conda env create -n csc -f environment.yml
conda activate csc
pip install .
You also need to generate the samtools and bowtie2 indices for your reference genome. We ship a copy of NC_045512 and a script to generate these indices:
conda activate csc
cd ref
./build_indices.sh
cd ..
Usage
Assuming you used above instructions to install via conda, you can run the tool like this:
conda activate csc
covid-spike-classification --reference /path/to/your/reference.fasta --outdir /path/to/result/dir /path/to/sanger/reads/dir_or.zip
Notably, you can provide the input either as a ZIP file or as a directory, as long as they directly contain the ab1 files you want to run the analysis on.
See also the --help
output for more detailed usage information.
License
All code is available under the Apache License version 2, see the
LICENSE
file for details.
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