HIV consensus calling

Molecular epidemiology of HIV-1 in Oryol Oblast, Russia

This repository contains iterative consensus calling pipeline used in 10.1101/2021.10.26.21265513. The pipeline consists of the two parts:

blastn sequencing reads of a sample against a set of curated reference HIV genomes to identify the closest reference sequence
iterative mapping and variant calling of sequencing reads on the selected reference sequence

Name		Name	Last commit message	Last commit date
Latest commit History 15 Commits
README.md		README.md
call_degenerate_cons.py		call_degenerate_cons.py
run_blast.sh		run_blast.sh
run_iterative_calling.sh		run_iterative_calling.sh