A pipeline to characterize and cluster plant NBS-LRR (NB-LRR) genes, phylogenetic analysis and visualization

This package is dependent on a list of open source packages:

• Required packages
  • Perl5
  • Python 2.7
  • HMMER v3.1
  • ClustalO v1.1.0
  • GNU Parallel
  • MUSCLE
  • PhyML
  • Most of these packages are available on MSI and can be checked and loaded by:

module show perl/python2/hmmer/clustalo/parallel/muscle/phyml
module load perl/python2/hmmer/clustalo/parallel/muscle/phyml

• Required perl modules
  • Bioperl
  • Data::Table
  • List::MoreUtils
  • Time::HiRes
  • Data::Dumper The BioPerl module has been installed on MSI and can be loaded by:

module load bioperl

Note that the $PERL5LIB environment variable needs to be set to include the source folder:

export export PERL5LIB=$PATH_TO_rgeneclust:$PERL5LIB

where $PATH_TO_rgeneclust is the absolute path of the source directory

• Required python packages:
  • numpy
  • pyfasta 0.5

Both python packages can be installed by pip:

pip install pyfasta
pip install numpy

By default pip will install packages into /usr/local, but you will probably need to install into user directories:

pip install --user pyfasta

usage: rosar.py [-h] [--cpu NCPU] cfgfile outdir

Identify, cluster and characterize plant NBS-LRR genes

positional arguments:
  cfgfile     config file (a text file with species identifier followed by the
              absolute path of CDS fasta in each line)
  outdir      output directory

optional arguments:
  -h, --help  show this help message and exit
  --cpu NCPU  number processors to use (default: all/24)

Config file (test.csv): A text file with species identifier followed by the absolute path of CDS fasta in each line, for example:

Fv,/home/zhoup/test/fvesca_v1.0_genemark_hybrid.fna
Md,/home/zhoup/test/Malus_x_domestica.v1.0.consensus_CDS.fa
Pp,/home/zhoup/test/Prunus_persica_v1.0_CDS.fa

with paths of the grape, apple and pear CDS sequences.