Пакет: pbdagcon (0.3+git20180411.c14c422+dfsg-8 и другие)

[ Источник: 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.

Другие пакеты, относящиеся к pbdagcon

• dep: libblasr [x32]

  tools for aligning PacBio reads to target sequences

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

  tools for aligning PacBio reads to target sequences

• dep: libc6 (>= 2.16) [x32]

  библиотека GNU C: динамически подключаемые библиотеки
  также виртуальный пакет, предоставляемый libc6-udeb

  dep: libc6 (>= 2.28) [sh4]

  dep: libc6 (>= 2.33) [amd64, arm64, mips64el, ppc64el]

  dep: libc6 (>= 2.34) [riscv64]

  dep: libc6 (>= 2.7) [m68k]

• dep: libc6.1 (>= 2.33) [alpha]

  библиотека GNU C: динамически подключаемые библиотеки
  также виртуальный пакет, предоставляемый libc6.1-udeb

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

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

  вспомогательная библиотека GCC

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

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

• dep: libgcc1 (>= 1:3.4) [x32]

  Пакет недоступен

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

• dep: libgcc2 (>= 4.2.1) [m68k]

  Пакет недоступен

• 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]

  Пакет недоступен

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

  Пакет недоступен

• dep: libpbbam2.0.0 (>= 2.0.0+dfsg) [alpha]

  Пакет недоступен

• dep: libpbbam2.1.0 (>= 2.1.0+dfsg) [ia64, riscv64]

  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~) [не m68k, sh4, x32]

• dep: libstdc++6 (>= 11) [mips64el]

  стандартная библиотека GNU C++ версии 3

  dep: libstdc++6 (>= 12) [не m68k, mips64el, 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]

  библиотека сжатия

• sug: blasr

  mapping single-molecule sequencing reads

Загрузка pbdagcon

Загрузить для всех доступных архитектур

Архитектура	Версия	Размер пакета	В установленном виде	Файлы
alpha (неофициальный перенос)	0.3+git20180411.c14c422+dfsg-8	350,4 Кб	1 534,0 Кб	[список файлов]
amd64	0.3+git20180411.c14c422+dfsg-8	347,1 Кб	1 294,0 Кб	[список файлов]
arm64	0.3+git20180411.c14c422+dfsg-8	313,9 Кб	1 218,0 Кб	[список файлов]
ia64 (неофициальный перенос)	0.3+git20180411.c14c422+dfsg-8	425,3 Кб	2 622,0 Кб	[список файлов]
m68k (неофициальный перенос)	0.3+git20161121.0000000+ds-1.1+b1	251,6 Кб	989,0 Кб	[список файлов]
mips64el	0.3+git20180411.c14c422+dfsg-8	316,4 Кб	1 556,0 Кб	[список файлов]
ppc64el	0.3+git20180411.c14c422+dfsg-8	361,7 Кб	1 650,0 Кб	[список файлов]
riscv64 (неофициальный перенос)	0.3+git20180411.c14c422+dfsg-8+b1	326,9 Кб	1 060,0 Кб	[список файлов]
sh4 (неофициальный перенос)	0.3+git20161121.0000000+ds-1.1+b1	301,0 Кб	905,0 Кб	[список файлов]
x32 (неофициальный перенос)	0~20160325+ds-1	188,4 Кб	500,0 Кб	[список файлов]