Package: wnpp Severity: wishlist Subject: ITP: mashmap -- mapping whole genomes or long reads (PacBio/ONT) to reference Package: wnpp Owner: Steffen Moeller <moel...@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