[Debian-med-packaging] Bug#990851: ITP: nano-snakemake -- detection of structural variants in genome sequencing data

[Steffen Moeller]

Package: wnpp
Severity: wishlist

Subject: ITP: nano-snakemake -- detection of structural variants in genome sequencing data
Package: wnpp
Owner: Steffen Moeller <moeller at debian.org>
Severity: wishlist

* Package name    : nano-snakemake
  Version         : 1.0+git20200224.ff11b35
  Upstream Author : Wouter De Coster
* URL             : https://github.com/wdecoster/nano-snakemake
* License         : Expat
  Programming Lang: Python
  Description     : detection of structural variants in genome sequencing data
 To "have a genetic variation" may mean many different things. Technically
 most straight forward to investigate are changes to single positions in
 the long DNA chains - every chromosome is a single polymer of nucleic acids.
 This is also what we have most data from for many diseases.
 .
 But sometimes, DNA that looks completely the same when looking at short reads
 at the time (and not feeling lucky), the position looked at may be inverted
 on the chromosome. Or it may be a copy of the original site and not a "real"
 single-nucleotide polymorphism (SNP). Or it may have translocated to
 another chromosome.
 .
 These are examples for structural changes to the DNA. Individuals may never
 notice them. Or there may be a higher chances to develop a disease or it may
 affect fertility. Technologies like the Nanopore have emerged that can read
 longer segments of the DNA, so one can see multiple copies of the same gene
 in the same read or at least can assemble the DNA fragments read in a way to
 then align the reads non-ambiguously and support the analysis of such
 copy-number variations (CNVs).
 .
 This snakemake pipeline on nanopore whole genome sequencing data provides
 a complete structural variant analysis. Steps implemented and tools
 wrapped comprise:
  * fast: minimap2 alignment with Sniffles and SVIM SV calling
  * precise: ngmlr alignment with Sniffles SV calling
  * minimap2: minimap2 alignment with Sniffles, SVIM, NanoSV and npInv SV calling
  * minimap2_pbsv: minimap2 alignment with pbsv-specific parameters with
    pbsv, SVIM, NanoSV and npInv SV calling
  * ngmlr: ngmlr with Sniffles, NanoSV, SVIM and npInv SV calling
  * last-prepare: create a LAST index and train aligner parameters using last-train
  * last: LAST alignment with tandem-genotypes STR calling

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