A merged read deduplication tool capable to perform merged read deduplication on single end data.
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README.md

DeDup

A merged read deduplication tool capable to perform merged read deduplication on single end data.

Build Status codecov install with bioconda

Author: Alexander Peltzer alexander.peltzer@uni-tuebingen.de

Method

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:

  • F_
  • R_
  • M_

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/