Paquet : pbdagcon (0.3+git20180411.c14c422+dfsg-9 et autres)

[ Paquet 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.

Autres paquets associés à pbdagcon

• dep: libblasr [x32]

  outils pour l'alignement de lectures PacBio sur des séquences cibles

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

  outils pour l'alignement de lectures PacBio sur des séquences cibles

• dep: libc6 (>= 2.16) [x32]

  bibliothèque C GNU : bibliothèques partagées
  un paquet virtuel est également fourni par 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]

  bibliothèque C GNU : bibliothèques partagées
  un paquet virtuel est également fourni par libc6.1-udeb

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

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

  bibliothèque de prise en charge de GCC

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

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

• dep: libgcc1 (>= 1:3.4) [x32]

  Paquet indisponible

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

• dep: libgcc2 (>= 4.2.1) [m68k]

  Paquet indisponible

• 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]

  Paquet indisponible

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

  Paquet indisponible

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

  Pacific Biosciences binary alignment/map (BAM) library

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

  Pacific Biosciences binary alignment/map (BAM) library

• dep: libpbdata [x32]

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• dep: libpbseq [m68k, sh4]

  library for analyzing PacBio sequencing data

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

• dep: libstdc++6 (>= 12) [ia64]

  bibliothèque standard C++ de GNU v3

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

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

• dep: libunwind8 [ia64]

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

  Bibliothèque de compression - binaires

• sug: blasr

  correspondance de lectures de séquençage de molécules simples

Télécharger pbdagcon

Télécharger pour toutes les architectures proposées

Architecture	Version	Taille du paquet	Espace occupé une fois installé	Fichiers
alpha (portage non officiel)	0.3+git20180411.c14c422+dfsg-9	330,0 ko	1 462,0 ko	[liste des fichiers]
amd64	0.3+git20180411.c14c422+dfsg-9	356,0 ko	1 330,0 ko	[liste des fichiers]
arm64	0.3+git20180411.c14c422+dfsg-9	319,1 ko	1 330,0 ko	[liste des fichiers]
ia64 (portage non officiel)	0.3+git20180411.c14c422+dfsg-8	425,3 ko	2 622,0 ko	[liste des fichiers]
m68k (portage non officiel)	0.3+git20161121.0000000+ds-1.1+b1	251,6 ko	989,0 ko	[liste des fichiers]
mips64el	0.3+git20180411.c14c422+dfsg-9	318,0 ko	1 582,0 ko	[liste des fichiers]
ppc64el	0.3+git20180411.c14c422+dfsg-9	357,5 ko	1 586,0 ko	[liste des fichiers]
riscv64	0.3+git20180411.c14c422+dfsg-9	340,2 ko	1 030,0 ko	[liste des fichiers]
sh4 (portage non officiel)	0.3+git20161121.0000000+ds-1.1+b1	301,0 ko	905,0 ko	[liste des fichiers]
x32 (portage non officiel)	0~20160325+ds-1	188,4 ko	500,0 ko	[liste des fichiers]