NAME

SYNOPSIS

  newblerAssemSubProject.pl [options] <subdirectory list> <sffInfo file>
  Options:
  -o <dir>      output assembly directory (optional) default=Newbler
  -p <dir>      location of phd_dir if you have finishing data in the assembly
  -fn <file>    finishing data output filename.  Default=finishingData
  -log <file>   log file (optional; default is newblerAssemSubProject.pl.log)
  -warn <file>  warning file (optional; default is defined in gapRes.config)
  -d            debug printing            (optional)
  -h            detailed message          (optional)

DESCRIPTION

This program takes a list of gap project subdirectories as well as an sffInfo file, which lists the name and locations of each sff file for the project, and converts any reads specified in a read list into sff or fasta/qual depending on if it is a 454 or sanger type read. It organizes the data into three directories created within each gap subdirectory for paired 454 data, unpaired 454 data, and sanger-type data (fasta/quals). If you have any finishing read data you must specify -p <phd_dir> so the program can find phd files associated with that data to create fasta and quals.

The organized read data for each gap subproject is then assembled with newbler. It finds the location of newblers runAssembly using the config file param "newblerEnv" which points to the isntallation of newbler. This is also used to set the env variable SFFFILE_PATH needed by reads2sff. The assembly output can be found in a directory within each gap subdirectory and its name is configurable (default = Newbler).

A default config file named gapRes.config residing in <installPath>/config is used to specify the following parameters:

  script.reads2sff=reads2sff.pl
  newblerAssemSubProject.newbler=<path to newbler>
  newblerAssemSubProject.newblerOptions=-consed -g -nrm -rip
  newblerAssemSubProject.pairedDataDir=pairedData
  newblerAssemSubProject.unpairedDataDir=unpairedData

If the value of the config parameter script.nnnn doesn't contain file paths, newblerAssemSubProject.pl assumes that the script name resides in the <installPath>/bin directory.

VERSION

$Revision: 1.18 $

$Date: 2010-03-06 14:38:48 $

AUTHOR(S)

HISTORY