isovic / sam2json

Overlapper evaluation from read-to-reference alignment

sam2json

This tool takes in a SAM file of read to reference alignments, and finds overlaps and stores them to a JSON format for easy parsing in Python. Intended for evaluating overlaps.

Install

https://github.com/isovic/sam2json.git & make modules & make  

Usage

To create JSON file for overlap evaluation, run:

bin/sam2json -f reads.fastq -i reads.sam -o reads.json  

To evaluate a MHAP file of overlaps overlaps.mhap against a pre-calculated truths JSON file reads.json, run:

./eval-mhap.py -j reads.json -i overlaps.mhap -o overlaps.eval  

Alignments can be generated using multiple aligners, e.g. GraphMap, BWA-MEM and LAST:

bin/sam2json -f reads.fastq -i graphmap.sam -o graphmap.json  
bin/sam2json -f reads.fastq -i bwamem.sam -o bwamem.json  
bin/sam2json -f reads.fastq -i last.sam -o last.json  

An overlap file can then be evaluated against all three at the same time:

./eval-mhap.py -g graphmap.json -b bwamem.json -l last.json -i overlaps.mhap -o overlaps.eval  

JSON format

JSON file contains a dictionary of pairs:

• key - ID of a read for which a list of overlapping reads is given,
• value - an array of IDs of reads with which the key read has an overlap with.