Пакунок: pbdagcon (0.3+git20180411.c14c422+dfsg-9 and others)

[ Source: 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.

Інші пакунки пов'язані з pbdagcon

• dep: libblasr [x32]

  tools for aligning PacBio reads to target sequences

• dep: libblasr5.3.5 (>= 5.3.5+dfsg) [not m68k, sh4, x32]

  tools for aligning PacBio reads to target sequences

• dep: libc6 (>= 2.16) [x32]

  Бібліотека GNU C: спільні бібліотеки
  also a virtual package provided by libc6-udeb

  dep: libc6 (>= 2.28) [sh4]

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

  dep: libc6 (>= 2.40) [loong64]

  dep: libc6 (>= 2.7) [m68k]

• dep: libc6.1 (>= 2.36) [ia64]

  Бібліотека GNU C: спільні бібліотеки
  also a virtual package provided by libc6.1-udeb

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

• dep: libgcc-s1 (>= 3.0) [arm64, loong64, ppc64el]

  Допоміжна бібліотека GCC

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

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

• dep: libgcc1 (>= 1:3.4) [x32]

  Пакунок недоступний

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

• dep: libgcc2 (>= 4.2.1) [m68k]

  Пакунок недоступний

• 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]

  Пакунок недоступний

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

  Пакунок недоступний

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

  Pacific Biosciences binary alignment/map (BAM) library

• dep: libpbbam2.4.0 (>= 2.4.0+dfsg) [not ia64, m68k, sh4, x32]

  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~) [not m68k, sh4, x32]

• dep: libstdc++6 (>= 12) [ia64]

  Стандартна бібліотека C++ GNU, версії 3

  dep: libstdc++6 (>= 14) [not ia64, m68k, sh4, x32]

  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]

  Бібліотека стискання даних (виконавчий модуль)

• sug: blasr

  mapping single-molecule sequencing reads

Завантажити pbdagcon

Завантаження для всіх доступних архітектур

Архітектура	Версія	Розмір пакунка	Розмір після встановлення	Файли
alpha (unofficial port)	0.3+git20180411.c14c422+dfsg-9	330.0 kB	1,462.0 kB	[список файлів]
amd64	0.3+git20180411.c14c422+dfsg-9	356.0 kB	1,330.0 kB	[список файлів]
arm64	0.3+git20180411.c14c422+dfsg-9	319.1 kB	1,330.0 kB	[список файлів]
ia64 (unofficial port)	0.3+git20180411.c14c422+dfsg-8	425.3 kB	2,622.0 kB	[список файлів]
loong64 (unofficial port)	0.3+git20180411.c14c422+dfsg-9	334.7 kB	1,314.0 kB	[список файлів]
m68k (unofficial port)	0.3+git20161121.0000000+ds-1.1+b1	251.6 kB	989.0 kB	[список файлів]
mips64el	0.3+git20180411.c14c422+dfsg-9	318.0 kB	1,582.0 kB	[список файлів]
ppc64el	0.3+git20180411.c14c422+dfsg-9	357.5 kB	1,586.0 kB	[список файлів]
riscv64	0.3+git20180411.c14c422+dfsg-9	340.2 kB	1,030.0 kB	[список файлів]
sh4 (unofficial port)	0.3+git20161121.0000000+ds-1.1+b1	301.0 kB	905.0 kB	[список файлів]
x32 (unofficial port)	0~20160325+ds-1	188.4 kB	500.0 kB	[список файлів]