WGS-assembler

Celera Assembler (CA) is a whole-genome shotgun (WGS) assembler for the reconstruction of genomic DNA sequence from WGS sequencing data.

Install

wget http://garr.dl.sourceforge.net/project/wgs-assembler/wgs-assembler/wgs-7.0/wgs-7.0-PacBio-Linux-amd64.tar.bz2
bzip2 -dc wgs-7.0-PacBio-Linux-amd64.tar.bz2  |  tar  -xf  -
mv wgs-7.0 /usr/local/bin/
chown -R root:root /usr/local/bin/wgs-7.0

Patch correctPacBio

wget http://www.cbcb.umd.edu/software/PBcR/data/correctPacBio
mv /usr/local/bin/wgs-7.0/Linux-amd64/bin/correctPacBio /usr/local/bin/wgs-7.0/Linux-amd64/bin/correctPacBio.OLD
mv correctPacBio /usr/local/bin/wgs-7.0/Linux-amd64/bin/
chmod 755 /usr/local/bin/wgs-7.0/Linux-amd64/bin/correctPacBio

Test

/usr/local/bin/wgs-7.0/Linux-amd64/bin/pacBioToCA 

usage: /usr/local/bin/wgs-7.0/Linux-amd64/bin/pacBioToCA [options] -s spec.file -fastq fastqfile <frg>
  -length                  Minimum length to keep.
  -partitions              Number of partitions for consensus
  -sge                     Submit consensus jobs to the grid
  -sgeCorrection           Parameters for the correction step for the grid. This should match the threads specified below, for example by using -pe threaded
  -l libraryname           Name of the library; freeformat text.
  -t threads               Number of threads to use for correction.