HaploClique 1.3.1 – Viral Quasispecies Assembly from Paired-end data

HaploClique 1.3.1

:: DESCRIPTION

HaploClique is a computational approach to reconstruct the structure of a viral quasispecies from next-generation sequencing data as obtained from bulk sequencing of mixed virus samples.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 HaploClique

:: MORE INFORMATION

Citation:

Viral quasispecies assembly via maximal clique enumeration.
Töpfer A, Marschall T, Bull RA, Luciani F, Schönhuth A, Beerenwinkel N.
PLoS Comput Biol. 2014 Mar 27;10(3):e1003515. doi: 10.1371/journal.pcbi.1003515.

BreakDancer 1.4.5 – Structural Variation Caller for Paired-end Data

BreakDancer 1.4.5

:: DESCRIPTION

BreakDancer is a  package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.

::DEVELOPER

The Genome Institute at Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Perl/C++

:: DOWNLOAD

 BreakDancer

:: MORE INFORMATION

Citation:

Ken Chen, John W Wallis, Michael D McLellan, David E Larson, Joelle M Kalicki, Craig S Pohl, Sean D McGrath, Michael C Wendl, Qunyuan Zhang2, Devin P Locke, Xiaoqi Shi, Robert S Fulton, Timothy J Ley, Richard K Wilson, Li Ding1 & Elaine R Mardis1
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation
Nature Methods 6, 677 – 681 (2009)