[Debian-med-packaging] Bug#993268: ITP: mashmap -- mapping whole genomes or long reads (PacBio/ONT) to reference

[Steffen Moeller]

Package: wnpp
Severity: wishlist

Subject: ITP: mashmap -- mapping whole genomes or long reads (PacBio/ONT) to reference
Package: wnpp
Owner: Steffen Moeller <moeller at debian.org>
Severity: wishlist

* Package name    : mashmap
  Version         : 2.0
  Upstream Author : Copyright: <years> <put author's name and email here>
* URL             : https://github.com/marbl/MashMap
* License         : PD
  Programming Lang: C
  Description     : mapping whole genomes or long reads (PacBio/ONT) to reference
 MashMap implements a fast and approximate algorithm for computing local
 alignment boundaries between long DNA sequences. It can be useful
 for mapping genome assembly or long reads (PacBio/ONT) to reference
 genome(s). Given a minimum alignment length and an identity threshold
 for the desired local alignments, Mashmap computes alignment boundaries
 and identity estimates using k-mers. It does not compute the alignments
 explicitly, but rather estimates a k-mer based Jaccard similarity using
 a combination of Minimizers and MinHash. This is then converted to an
 estimate of sequence identity using the Mash distance. An appropriate
 k-mer sampling rate is automatically determined using the given minimum
 local alignment length and identity thresholds. The efficiency of the
 algorithm improves as both of these thresholds are increased.

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/mashmap