Package: wnpp Severity: wishlist Subject: ITP: mosdepth -- BAM/CRAM depth calculation biological sequencing Package: wnpp Owner: Steffen Moeller <moel...@debian.org> Severity: wishlist
* Package name : mosdepth Version : 0.3.1 Upstream Author : Brent Pedersen * URL : https://github.com/brentp/mosdepth * License : Expat Programming Lang: Python Description : BAM/CRAM depth calculation biological sequencing Many small reads are produced by high-throughput "next generation" sequencing technologies. The final sequence is derived from how these reads are overlapping towards a consensus. The more reads are covering/confirming parts of a nucleotide seq, the higher the confidence is. Too many reads would be indicative of e.g. repeats in the genome. . mosdepth can output: * per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome. * mean per-window depth given a window size--as would be used for CNV calling. * the mean per-region given a BED file of regions. * a distribution of proportion of bases covered at or above a given threshhold for each chromosome and genome-wide. * quantized output that merges adjacent bases as long as they fall in the same coverage bins e.g. (10-20) * threshold output to indicate how many bases in each region are covered at the given thresholds. when appropriate, the output files are bgzipped and indexed for ease of use. Remark: This package is maintained by Debian Med Packaging Team at https://salsa.debian.org/med-team/mosdepth