[Debian-med-packaging] Bug#808895: ITP: lofreq -- sensitive variant calling from sequencing data

[Afif Elghraoui]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>

* Package name    : lofreq
  Version         : 2.1.2
  Upstream Author : Andreas Wilm and Niranjan Nagarajan <lofreq-help at lists.sourceforge.net>
* URL             : http://csb5.github.io/lofreq
* License         : MIT
  Programming Lang: C, Python
  Description     : sensitive variant calling from sequencing data

 LoFreq* (i.e. LoFreq version 2) is a fast and sensitive
 variant-caller for inferring SNVs and indels from next-generation
 sequencing data. It makes full use of base-call qualities and other
 sources of errors inherent in sequencing (e.g. mapping or base/indel
 alignment uncertainty), which are usually ignored by other methods or
 only used for filtering.
 .
 LoFreq* can run on almost any type of aligned sequencing data
 (e.g. Illumina, IonTorrent or Pacbio) since no machine- or
 sequencing-technology dependent thresholds are used. It automatically
 adapts to changes in coverage and sequencing quality and can
 therefore be applied to a variety of data-sets e.g.
 viral/quasispecies, bacterial, metagenomics or somatic data.
 .
 LoFreq* is very sensitive; most notably, it is able to predict
 variants below the average base-call quality (i.e. sequencing error
 rate). Each variant call is assigned a p-value which allows for
 rigorous false positive control. Even though it uses no
 approximations or heuristics, it is very efficient due to several
 runtime optimizations and also provides a (pseudo-)parallel
 implementation. LoFreq* is generic and fast enough to be applied to
 high-coverage data and large genomes. On a single processor it takes
 a minute to analyze Dengue genome sequencing data with nearly 4000X
 coverage, roughly one hour to call SNVs on a 600X coverage E.coli
 genome and also roughly an hour to run on a 100X coverage human exome
 dataset.



This package will be maintained by the Debian Med team.