Bug#813385: ITP: reapr -- universal tool for genome assembly evaluation

[Sascha Steinbiss <satta@tetrinetsucht.de>]

Package: wnpp
Severity: wishlist
Owner: Sascha Steinbiss <satta@tetrinetsucht.de>

* Package name    : reapr
  Version         : 1.0.18 
  Upstream Author : Martin Hunt <martin.hunt@sanger.ac.uk> 
* URL             : http://www.sanger.ac.uk/science/tools/reapr 
* License         : GPL
  Programming Lang: C++, Perl
  Description     : universal tool for genome assembly evaluation

REAPR is a tool that evaluates the accuracy of a genome assembly using mapped
paired end reads, without the use of a reference genome for comparison. It can
be used in any stage of an assembly pipeline to automatically break incorrect
scaffolds and flag other errors in an assembly for manual inspection. It
reports mis-assemblies and other warnings, and produces a new broken assembly
based on the error calls.
The software requires as input an assembly in FASTA format and paired reads
mapped to the assembly in a BAM file. Mapping information such as the fragment
coverage and insert size distribution is analysed to locate mis-assemblies.
REAPR works best using mapped read pairs from a large insert library (at least
1000bp). Additionally, if a short insert Illumina library is also available,
REAPR can combine this with the large insert library in order to score each
base of the assembly.

This package will be maintained under the umbrella of the Debian Med Packaging
Team.