Balík: pbdagcon (0.3+git20180411.c14c422+dfsg-9 a iné)

[ Zdroj: 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.

Ostatné balíky súvisiace s balíkom pbdagcon

• dep: libblasr [x32]

  tools for aligning PacBio reads to target sequences

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

  tools for aligning PacBio reads to target sequences

• dep: libc6 (>= 2.16) [x32]

  knižnica GNU C - zdieľané knižnice
  tiež virtuálny balík poskytovaný balíkom 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]

  knižnica GNU C - zdieľané knižnice
  tiež virtuálny balík poskytovaný balíkom libc6.1-udeb

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

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

  podporná knižnica GCC

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

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

• dep: libgcc1 (>= 1:3.4) [x32]

  Balík nie je dostupný

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

• dep: libgcc2 (>= 4.2.1) [m68k]

  Balík nie je dostupný

• 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]

  Balík nie je dostupný

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

  Balík nie je dostupný

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

  Pacific Biosciences binary alignment/map (BAM) library

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

• dep: libstdc++6 (>= 12) [ia64]

  štandardná knižnica C++ GNU v3

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

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

• dep: libunwind8 [ia64]

  nnižnica na určenie na určenie postupnosti volania programu - dynamické súbory

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

  komprimačná knižnica - dynamická verzia

• sug: blasr

  mapping single-molecule sequencing reads

Stiahnuť pbdagcon

Stiahnuť pre všetky dostupné architektúry

Architektúra	Verzia	Veľkosť balíka	Nainštalovaná veľkosť	Súbory
alpha (neoficiálny port)	0.3+git20180411.c14c422+dfsg-9	330.0 kB	1,462.0 kB	[zoznam súborov]
amd64	0.3+git20180411.c14c422+dfsg-9	356.0 kB	1,330.0 kB	[zoznam súborov]
arm64	0.3+git20180411.c14c422+dfsg-9	319.1 kB	1,330.0 kB	[zoznam súborov]
ia64 (neoficiálny port)	0.3+git20180411.c14c422+dfsg-8	425.3 kB	2,622.0 kB	[zoznam súborov]
loong64 (neoficiálny port)	0.3+git20180411.c14c422+dfsg-9	334.7 kB	1,314.0 kB	[zoznam súborov]
m68k (neoficiálny port)	0.3+git20161121.0000000+ds-1.1+b1	251.6 kB	989.0 kB	[zoznam súborov]
mips64el	0.3+git20180411.c14c422+dfsg-9	318.0 kB	1,582.0 kB	[zoznam súborov]
ppc64el	0.3+git20180411.c14c422+dfsg-9	357.5 kB	1,586.0 kB	[zoznam súborov]
riscv64	0.3+git20180411.c14c422+dfsg-9	340.2 kB	1,030.0 kB	[zoznam súborov]
sh4 (neoficiálny port)	0.3+git20161121.0000000+ds-1.1+b1	301.0 kB	905.0 kB	[zoznam súborov]
x32 (neoficiálny port)	0~20160325+ds-1	188.4 kB	500.0 kB	[zoznam súborov]