A merged read deduplication tool capable to perform merged read deduplication on single end data.
Author: Alexander Peltzer firstname.lastname@example.org
The DeDup tool is designed to work with forward, reverse and merged reads (forward and reverse combined to make a single read). DeDup expects the different kinds of reads to have read names that begin with one of the following prefixes:
To remove PCR duplicates we only retain a single read for a given genomic position and read direction. For M_ (merged) reads we know both the start and end of the sequenced fragment. For F_ and R_ reads we only know the start or end of the sequenced fragment becuase the read length is variable.
A little documentation is available at http://dedup.readthedocs.io/en/latest/