Paket: pbdagcon (0.3+git20180411.c14c422+dfsg-1 und andere)

[ Quellcode: 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.

Andere Pakete mit Bezug zu pbdagcon

• dep: libblasr5.3.4 (>= 5.3.4+dfsg)

  tools for aligning PacBio reads to target sequences

• dep: libc6 (>= 2.14) [amd64]

  GNU-C-Bibliothek: Laufzeitbibliotheken
  auch ein virtuelles Paket, bereitgestellt durch libc6-udeb

  dep: libc6 (>= 2.17) [arm64, ppc64el]

  dep: libc6 (>= 2.7) [mips64el]

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

  GCC Support-Bibliothek

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

• dep: libpbseq (>= 5.3.3)

  library for analyzing PacBio sequencing data

• dep: libstdc++6 (>= 9)

  GNU-Implementierung der Standard-C++-Bibliothek (Version 3)

• sug: blasr

  mapping single-molecule sequencing reads

pbdagcon herunterladen

Download für alle verfügbaren Architekturen

Architektur	Version	Paketgröße	Größe (installiert)	Dateien
amd64	0.3+git20180411.c14c422+dfsg-1+b1	335,8 kB	1.239,0 kB	[Liste der Dateien]
arm64	0.3+git20180411.c14c422+dfsg-1+b1	304,2 kB	1.159,0 kB	[Liste der Dateien]
mips64el	0.3+git20180411.c14c422+dfsg-1+b1	311,7 kB	1.525,0 kB	[Liste der Dateien]
ppc64el	0.3+git20180411.c14c422+dfsg-1+b1	349,9 kB	1.583,0 kB	[Liste der Dateien]