Paketti: pbdagcon (0.3+git20180411.c14c422+dfsg-9 ja muut)

[ 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.

Muut pakettiin pbdagcon liittyvät paketit

• dep: libblasr [x32]

  tools for aligning PacBio reads to target sequences

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

  tools for aligning PacBio reads to target sequences

• dep: libc6 (>= 2.16) [x32]

  GNU-C-kirjasto: jaetut kirjastot
  myös näennäispaketti, jonka toteuttaa 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-kirjasto: jaetut kirjastot
  myös näennäispaketti, jonka toteuttaa libc6.1-udeb

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

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

  GCC:n apukirjasto

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

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

• dep: libgcc1 (>= 1:3.4) [x32]

  Paketti ei saatavilla

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

• dep: libgcc2 (>= 4.2.1) [m68k]

  Paketti ei saatavilla

• 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]

  Paketti ei saatavilla

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

  Paketti ei saatavilla

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

  Pacific Biosciences binary alignment/map (BAM) library

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

• dep: libstdc++6 (>= 12) [ia64]

  GNU standardi C++ -kirjasto, versio 3

  dep: libstdc++6 (>= 14) [ei 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]

  pakkauskirjaston ajonaikaistiedostot

• sug: blasr

  mapping single-molecule sequencing reads

Imuroi pbdagcon

Imurointi kaikille saataville arkkitehtuureille

Arkkitehtuuri	Versio	Paketin koko	Koko asennettuna	Tiedostot
alpha (epävirallinen siirros)	0.3+git20180411.c14c422+dfsg-9	330.0 kt	1,462.0 kt	[tiedostoluettelo]
amd64	0.3+git20180411.c14c422+dfsg-9	356.0 kt	1,330.0 kt	[tiedostoluettelo]
arm64	0.3+git20180411.c14c422+dfsg-9	319.1 kt	1,330.0 kt	[tiedostoluettelo]
ia64 (epävirallinen siirros)	0.3+git20180411.c14c422+dfsg-8	425.3 kt	2,622.0 kt	[tiedostoluettelo]
m68k (epävirallinen siirros)	0.3+git20161121.0000000+ds-1.1+b1	251.6 kt	989.0 kt	[tiedostoluettelo]
mips64el	0.3+git20180411.c14c422+dfsg-9	318.0 kt	1,582.0 kt	[tiedostoluettelo]
ppc64el	0.3+git20180411.c14c422+dfsg-9	357.5 kt	1,586.0 kt	[tiedostoluettelo]
riscv64	0.3+git20180411.c14c422+dfsg-9	340.2 kt	1,030.0 kt	[tiedostoluettelo]
sh4 (epävirallinen siirros)	0.3+git20161121.0000000+ds-1.1+b1	301.0 kt	905.0 kt	[tiedostoluettelo]
x32 (epävirallinen siirros)	0~20160325+ds-1	188.4 kt	500.0 kt	[tiedostoluettelo]