Pakiet: pbdagcon (0.3+git20161121.0000000+ds-1.1)

[ Pakiet źródłowy: 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.

Inne pakiety związane z pbdagcon

• dep: libc6 (>= 2.17)

  Biblioteka GNU C: biblioteki współdzielone
  również pakiet wirtualny udostępniany przez libc6-udeb

• dep: libgcc1 (>= 1:3.0)

  Biblioteka wspomagająca GCC

• dep: libhdf5-103

  Hierarchical Data Format 5 (HDF5) - pliki uruchomieniowe - wydanie szeregowe

• dep: libhdf5-cpp-103 (>= 1.8.13)

  Hierarchical Data Format 5 (HDF5) - C++ libraries

• dep: libhts2 (>= 1.0)

  C library for high-throughput sequencing data formats

• dep: libpbbam0.19.0 (>= 0.19.0+dfsg)

  Pacific Biosciences binary alignment/map (BAM) library

• dep: libpbseq

  library for analyzing PacBio sequencing data

• dep: libstdc++6 (>= 6)

  Standardowa biblioteka GNU C++, wersja 3

• dep: zlib1g (>= 1:1.1.4)

  Biblioteka kompresyjna - pliki wykonawcze

• sug: blasr

  mapping single-molecule sequencing reads

Pobieranie pbdagcon

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