NAME

createGapResProject.pl - wrapper program to prepare and creates sub project directories for gap resolution.

SYNOPSIS

  createGapResProject.pl [options] <aceFile> <454Scaffold.txt> <454NewblerMetrics.txt>
  Options:
  -od <directory>  Output directory (optional; default is current working directory).
  -h               Detailed message (optional)

DESCRIPTION

This program reads an agp formatted file (i.e., 454Scaffold.txt) and constructs a sub project directory for each gap in all scaffolds that are larger than N (configurable) and have more than one contig. The two contigs spanning the gap must have at least M (configurable) number of linking reads for creation of the directory. Each directory contains a scaffinfo.txt file containing the information about the contig and gap size, formatted as such, whereby each item is separated by a tab, and represents one entry per line:

  1. gap name
  2. gap size
  3. left contig length
  4. left contig name
  5. right contig length
  6. right contig name
  7. scaffold name

The program also creates the directory 'assemInfo' within the specified output directory containing the following files:

  * gapdirs.txt - list of sub project directories.
  * libinfo.txt - library name, insert size and standard deviation.  For more
  information on the format of this file, refer to the parseNewblerMetrics.pl
  documentation.
  
  * sffinfo.txt - sff name and location. For more information on the format of
  this file, refer to the parseNewblerMetrics.pl
  
  * readinfo.txt - read pairing information.  For more information on the format
  of this file, refer to the newblerAce2ReadPair.pl documentation.
  
  * contigOrientation.txt - file containing contig name and orientation (+/-)
  delimited by a tab, one per line.
  
The program acts as a wrapper that calls the following executables:
  1. newblerAce2ReadPair.pl
  2. parseNewblerMetrics.pl
  3. createSubProject.pl
  
A default config file named gapRes.config residing in
<installPath>/config is used to specify the following parameters:
  createSubProject.minReadLinkage=minimum number of read links across gapped contigs
  createSubProject.minScaffSize=minimum scaffold size for sub project creation
  createSubProject.ignoreCircularGap=0|1 used to create sub project for circularized genomes
  script.readInfoFileGenerator=newblerAce2ReadPair.pl
  script.parseNewblerMetrics=parseNewblerMetrics.pl
  script.createSubProject=createSubProject.pl
  
If the value of the config parameter script.nnnn doesn't contain file paths, 
createGapResProject.pl assumes that the script name resides in the
<installPath>/bin directory.

VERSION

$Revision: 1.6 $

$Date: 2009-08-26 17:18:14 $

AUTHOR(S)

Stephan Trong

HISTORY