Balík: mosdepth (0.3.10+ds-1 a iné)

[ Zdroj: mosdepth  ]

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
    threshold 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.

Ostatné balíky súvisiace s balíkom mosdepth

• dep: libc6 (>= 2.33) [sparc64]

  knižnica GNU C - zdieľané knižnice
  tiež virtuálny balík poskytovaný balíkom libc6-udeb

  dep: libc6 (>= 2.34) [nie sparc64]

• dep: libhts-dev [nie sparc64]

  development files for the HTSlib

Stiahnuť mosdepth

Stiahnuť pre všetky dostupné architektúry

Architektúra	Verzia	Veľkosť balíka	Nainštalovaná veľkosť	Súbory
amd64	0.3.10+ds-1	170.2 kB	597.0 kB	[zoznam súborov]
arm64	0.3.10+ds-1	164.5 kB	597.0 kB	[zoznam súborov]
armel	0.3.10+ds-1	156.1 kB	557.0 kB	[zoznam súborov]
armhf	0.3.10+ds-1	159.2 kB	433.0 kB	[zoznam súborov]
i386	0.3.10+ds-1	182.6 kB	632.0 kB	[zoznam súborov]
mips64el	0.3.10+ds-1	154.8 kB	660.0 kB	[zoznam súborov]
ppc64 (neoficiálny port)	0.3.10+ds-1	177.7 kB	790.0 kB	[zoznam súborov]
ppc64el	0.3.10+ds-1	179.6 kB	725.0 kB	[zoznam súborov]
riscv64	0.3.10+ds-1	170.3 kB	501.0 kB	[zoznam súborov]
sparc64 (neoficiálny port)	0.3.3+ds-1	134.0 kB	543.0 kB	[zoznam súborov]