CovProfile: profiling the viral genome and gene expressions of SARS-COV-2
To get CovProfile, run the following command:
git clone https://github.com/yonghanyu/CovProfile.git
To see the options and usage for CovProfile:
cd CovProfile
python3 CovProfile.py --help
We recommend to use CovProfile with SARS-COV-2 reference file and gene annotation file from NCBI database
CovProfile currently support PCR captured Nanopore sequenced reads. The program require PCR primer information to run. Prepare your primer_information file with tsv format wtih the following header
name pool seq length
python version 3.5+ is required with package pysam, numpy, scipy and BCBio. To install them with pip, run the following command:
pip3 install pysam numpy scipy BCBio
Several software is required for CovProfile to perform alignment, processing bam file and call SNP:
##Cite CovProfile If you use CovProfile in your work, please cite with doi: doi.org/10.1101/2020.04.05.026146
This project is licensed under the MIT License - see the LICENSE.md file for details