SSDS pipeline Accessory Scripts:

Initial paper: Khil et al. Genome Research 2012

Technical paper: Brick, Pratto et al., Methods in Enzymology 2018

These scripts are part of the nf-core implementation of the SSDS pipeline. They can also be used stand-alone.

Requirements:

Python modules :
- biopython
- pysam
- pybedtools

parse_SSDS_BAM.py\

Parse the BWA-aligned BAM file from an SSDS experiment. Identifies DNA derived from ssDNA, dsDNA and other unclassifiable things. Outputs BED & BAM files for fragments of each type.

parse_SSDS_BAM.py
  --bam <<bam - BAM from BWA-alignment of SSDS reads>>
  --name <<output file prefix>>
  --vers <<show version>>

calculate_SPoT.py

Calculates the Signal Portion of Tags (SPoT) - actually fragments, but that's OK :) - for a given BED file of intervals. Generally used to check SSDS signal @ DSB hotspots / origins of replication.

calculate_SPoT.py
  --reads <<BED file of reads/fragments>>
  --intervals <<BED file of intervals to test>>
  --name <<sample name>>
  --iname <<intervals name>>
  --g <<genome index - FASTA.FAI file>>
  --o <<output report prefix - file will be $prefix.SSDS_SPoT_report.txt>>
  --norand <<do not get SPoT for a randomized set>>
  --vers <<show version>>