Duplex consensus sequences (DCS)

DCS_maker.py

Function: To generate duplex/double-strand consensus sequences for molecule based error suppression.

• Consensus sequence from bases with Phred quality >= 30
• Consensus quality score from addition of quality scores (i.e. product of error probabilities)

(Written for Python 3.5.1)

Usage: Python3 DCS_maker.py [–infile INFILE] [–outfile OUTFILE] [–bedfile BEDFILE]

Arguments:

–infile INFILE	input BAM file
–outfile OUTFILE	output BAM file
–bedfile BEDFILE	Bedfile containing coordinates to subdivide the BAM file (Recommendation: cytoband.txt)

Inputs:

1. A position-sorted BAM file containing paired-end reads with SSCS consensus identifier in the header/query name
2. A BED file containing coordinates subdividing the entire ref genome for more manageable data processing

Outputs:

1. A BAM file containing paired double stranded consensus sequences - “dcs.bam”
2. A SSCS singleton BAM file containing SSCSs without reads from the complementary strand - “sscs.singleton.bam”
3. A text file containing summary statistics (Total SSCS reads, Unmmaped SSCS reads, Secondary/Supplementary SSCS reads, DCS reads, and SSCS singletons) - “stats.txt” (Stats pended to same stats file as SSCS)

Concepts:

• Read family: reads that share the same molecular barcode, chr, and start coordinates for Read1 and Read2
• SSCS Singleton: a SSCS read without its complementary read