Package: wnpp Severity: wishlist Subject: ITP: nano-snakemake -- detection of structural variants in genome sequencing data Package: wnpp Owner: Steffen Moeller <moel...@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