Paket: pbdagcon (0.3+git20180411.c14c422+dfsg-9 ve diğerleri)

[ Kaynak: pbdagcon  ]

sequence consensus using directed acyclic graphs

pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus) which is a sequence consensus algorithm based on using directed acyclic graphs to encode multiple sequence alignment.

It uses the alignment information from blasr to align sequence reads to a "backbone" sequence. Based on the underlying alignment directed acyclic graph (DAG), it will be able to use the new information from the reads to find the discrepancies between the reads and the "backbone" sequences. A dynamic programming process is then applied to the DAG to find the optimum sequence of bases as the consensus. The new consensus can be used as a new backbone sequence to iteratively improve the consensus quality.

While the code is developed for processing PacBio(TM) raw sequence data, the algorithm can be used for general consensus purpose. Currently, it only takes FASTA input. For shorter read sequences, one might need to adjust the blasr alignment parameters to get the alignment string properly.

The code and the underlying graphical data structure have been used for some algorithm development prototyping including phasing reads and pre-assembly.

pbdagcon ile İlgili Diğer Paketler

• dep: libblasr [x32]

  tools for aligning PacBio reads to target sequences

• dep: libblasr5.3.5 (>= 5.3.5+dfsg) [m68k, sh4, x32 değil]

  tools for aligning PacBio reads to target sequences

• dep: libc6 (>= 2.16) [x32]

  GNU C Library: Shared libraries
  ayrıca şunun tarafından sağlanan bir sanal paket libc6-udeb

  dep: libc6 (>= 2.28) [sh4]

  dep: libc6 (>= 2.38) [amd64, arm64, mips64el, ppc64el, riscv64]

  dep: libc6 (>= 2.7) [m68k]

• dep: libc6.1 (>= 2.36) [ia64]

  GNU C Library: Shared libraries
  ayrıca şunun tarafından sağlanan bir sanal paket libc6.1-udeb

  dep: libc6.1 (>= 2.38) [alpha]

• dep: libgcc-s1 (>= 3.0) [arm64, ppc64el]

  GCC support library

  dep: libgcc-s1 (>= 3.4) [alpha, amd64, mips64el, riscv64]

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

• dep: libgcc1 (>= 1:3.4) [x32]

  Paket mevcut değil

  dep: libgcc1 (>= 1:4.2) [sh4]

• dep: libgcc2 (>= 4.2.1) [m68k]

  Paket mevcut değil

• dep: libhdf5-103 [m68k, sh4]

  HDF5 C runtime files - serial version (transitional package)

• dep: libhdf5-cpp-103 (>= 1.8.13) [m68k, sh4]

  HDF5 - C++ runtime files - serial version (transitional package)

• dep: libhts2 (>= 1.0) [m68k, sh4]

  Paket mevcut değil

• dep: libpbbam0.23.0 (>= 0.23.0+dfsg) [m68k, sh4]

  Paket mevcut değil

• dep: libpbbam2.1.0 (>= 2.1.0+dfsg) [ia64]

  Pacific Biosciences binary alignment/map (BAM) library

• dep: libpbbam2.4.0 (>= 2.4.0+dfsg) [ia64, m68k, sh4, x32 değil]

  Pacific Biosciences binary alignment/map (BAM) library

• dep: libpbdata [x32]

  tools for handling PacBio sequences

• dep: libpbseq [m68k, sh4]

  library for analyzing PacBio sequencing data

  dep: libpbseq (>= 5.3.5+dfsg-4~) [m68k, sh4, x32 değil]

• dep: libstdc++6 (>= 12) [ia64]

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 14) [ia64, m68k, sh4, x32 değil]

  dep: libstdc++6 (>= 6) [m68k, sh4, x32]

• dep: libunwind8 [ia64]

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

• dep: zlib1g (>= 1:1.1.4) [m68k, sh4]

  compression library - runtime

• sug: blasr

  mapping single-molecule sequencing reads

pbdagcon indir

Tüm mevcut mimariler için indir

Mimari	Sürüm	Paket Boyutu	Kurulu Boyut	Dosyalar
alpha (resmi olmayan port)	0.3+git20180411.c14c422+dfsg-9	330,0 kB	1.462,0 kB	[dosya listesi]
amd64	0.3+git20180411.c14c422+dfsg-9	356,0 kB	1.330,0 kB	[dosya listesi]
arm64	0.3+git20180411.c14c422+dfsg-9	319,1 kB	1.330,0 kB	[dosya listesi]
ia64 (resmi olmayan port)	0.3+git20180411.c14c422+dfsg-8	425,3 kB	2.622,0 kB	[dosya listesi]
m68k (resmi olmayan port)	0.3+git20161121.0000000+ds-1.1+b1	251,6 kB	989,0 kB	[dosya listesi]
mips64el	0.3+git20180411.c14c422+dfsg-9	318,0 kB	1.582,0 kB	[dosya listesi]
ppc64el	0.3+git20180411.c14c422+dfsg-9	357,5 kB	1.586,0 kB	[dosya listesi]
riscv64	0.3+git20180411.c14c422+dfsg-9	340,2 kB	1.030,0 kB	[dosya listesi]
sh4 (resmi olmayan port)	0.3+git20161121.0000000+ds-1.1+b1	301,0 kB	905,0 kB	[dosya listesi]
x32 (resmi olmayan port)	0~20160325+ds-1	188,4 kB	500,0 kB	[dosya listesi]