Package: soapsnp (1.03-5 and others)

[ Source: soapsnp  ]

resequencing utility that can assemble consensus sequence of genomes

For getting ideas on the cause of diseases or their response to therapy, and for understanding either for a particular patient, doctors around the globe are starting to look at the genes or the whole genome and how that sequence is different from a healthy / well responding individual.

SOAPsnp is a member of the SOAP (Short Oligonucleotide Analysis Package). The program is a resequencing utility. It assembles the consensus sequence for the genome of a newly sequenced individual based on the alignment of the raw sequencing reads on a known reference. SNPs can then be identified on the consensus sequence through the comparison with the reference.

SOAPsnp uses a method based on Bayes' theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors. All these kinds of information was integrated into a single quality score for each base in PHRED scale to measure the accuracy of consensus calling. Currently, it supports the alignment format of SOAPaligner (soap2).

Other Packages Related to soapsnp

• dep: libc6 (>= 2.34) [not alpha, ia64, sh4]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

  dep: libc6 (>= 2.36) [sh4]

• dep: libc6.1 (>= 2.34) [alpha]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6.1-udeb

  dep: libc6.1 (>= 2.36) [ia64]

• dep: libgcc-s1 (>= 3.0) [not armel, armhf, hppa, i386, ia64, m68k, sh4]

  GCC support library

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

  dep: libgcc-s1 (>= 4.2) [i386, ia64, sh4]

• dep: libgcc-s2 (>= 4.2.1) [m68k]

  GCC support library

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC support library

• dep: libstdc++6 (>= 13.1) [riscv64]

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 5.2) [not riscv64]

• dep: libunwind8 [ia64]

  library to determine the call-chain of a program - runtime

• dep: zlib1g (>= 1:1.1.4) [sparc64]

  compression library - runtime

• sug: genomics.cn-soapsnp

  Package not available

Download soapsnp

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
alpha (unofficial port)	1.03-5	54.4 kB	146.0 kB	[list of files]
amd64	1.03-5	48.6 kB	118.0 kB	[list of files]
arm64	1.03-5	43.5 kB	146.0 kB	[list of files]
armel	1.03-5	41.2 kB	97.0 kB	[list of files]
armhf	1.03-5	40.3 kB	77.0 kB	[list of files]
hppa (unofficial port)	1.03-5	52.1 kB	111.0 kB	[list of files]
i386	1.03-5	48.6 kB	117.0 kB	[list of files]
ia64 (unofficial port)	1.03-5	70.3 kB	205.0 kB	[list of files]
m68k (unofficial port)	1.03-5	45.8 kB	113.0 kB	[list of files]
mips64el	1.03-5	49.3 kB	149.0 kB	[list of files]
ppc64 (unofficial port)	1.03-5	52.9 kB	146.0 kB	[list of files]
ppc64el	1.03-5	52.4 kB	146.0 kB	[list of files]
riscv64	1.03-5+b1	52.2 kB	95.0 kB	[list of files]
s390x	1.03-5	46.8 kB	122.0 kB	[list of files]
sh4 (unofficial port)	1.03-5	58.3 kB	145.0 kB	[list of files]
sparc64 (unofficial port)	1.03-5	42.1 kB	1,044.0 kB	[list of files]
x32 (unofficial port)	1.03-5	50.9 kB	113.0 kB	[list of files]