Singleton Correction

singleton_correction.py

Function: To correct single reads with its complementary (SSCS/singleton) strand and enable error suppression

• Traditionally, consensus sequences can only be made from 2 or more reads

(Written for Python 3.5.1)

Usage: Python3 singleton_correction.py [–singleton Singleton BAM] [–bedfile BEDFILE]

Arguments:

–singleton SingletonBAM	input singleton 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 single reads with barcode identifiers 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 singletons error corrected by its complementary SSCS - “sscs.correction.bam”
2. A BAM file containing paired singletons error corrected by its complementary singleton - “singleton.correction.bam”
3. A BAM file containing the remaining singletons that cannot be corrected as its missing a complementary strand - “uncorrected.bam”
4. A text file containing summary statistics (Total singletons, Singleton Correction by SSCS, % Singleton Correction by SSCS, Singleton Correction by Singletons, % Singleton Correction by Singletons, Uncorrected 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
• Singleton: single read with no PCR duplicates (family size = 1)