This set of scripts was developed to identify and to generate intrahost/co-infection consensus genomes of SARS-CoV-2. The test sequences were generate by reference genome assembly with bowtie2 usign the SRR13418742 data from Gupta et al. 2021 REF.

• This repository is out of date, the current development of this script was incorporated as a step of the workflow present in this link in python_scripts/intrahost.py.

This script need 2 pre-installed tools:

• bam-readcount
• MAFFT

With the bam-readcount and MAFFT intalled, you can use conda to install all dependencies:

conda env create -f mFinder.yml

conda activate mFinder

The main.sh compile all steps to perform the analysis, and 3 files should be parsed:

• reference = reference wuhan genome (NC_045512.2)

• consensus = the consensus genome that will be screened to intrahost variants

• sorted_bam = sorted bam file that was used to generate the consensus sequences

• Running

bash main.sh reference consensus sorted_bam

• Test files:

bash main.sh test_files/NC_045512v2.fa test_files/SRR13418742.consensus.fa test_files/SRR13418742.sorted.bam

• *.tsv.fmt.minors.tsv.fmt - tab separed file with the nucleotide diversity by intrahost variant postition, the nucleotide and depth of minor and major variants
• *.algn.major.fa - fasta alignment with the major variant consensus sequence
• *.algn.minor.fa - fasta alignment with the minor variant consensus sequence

• The name of consensus and sorted_bam files should contain the sequence name header of consenus sequences;
• This set of scripts didn't recovery intrahost variants related do indel regions, these region ones should be investigated manually.