Deep Mutational Scanning Analysis scripts
This is the pipeline used in the paper "Comprehensive fitness landscape of SARS-CoV-2 Mpro reveals insights into viral resistance mechanisms." It takes raw fastq files generated on Illumina deep sequencing platforms and counts Mpro alleles.
- 01_fastq_parse.pl
The 01_fastq_parse.pl script reads in the single end fastq file and outputs the barcodes and index sequences for each Mpro read:
usage: script.pl fastq PHRED_cutoff constant_check rev_comp(-1)
#read in single end fastq file and outputs sequences that match constant region and have PHRED>cutoff #output bc and index sequences to parsed files #output unparsed sequences as leftover.fastq
- sort output file by index
usage sort 01Mpro.out > 01Mpro_sort.out
- 02_parse_identifiers.pl
usage: script.pl 01Mpro_sort.out
#reads in sorted barcode file and for each index sequence outputs the tabulation of reads of each barocde as 02Mpro.out
- 03_tabulate_counts.pl
03_tabulate_counts.pl calls the 02Mpro.out flie and the barcode-ORF assembly file and outputs the tabluation for each mutation organized by position, amino acid, codon, for each index