NAME

newblerAce2ReadPair.pl

SYNOPSIS

  newblerAce2ReadPair.pl [options] <acefile> <outputfile>
  
  Options:
  -cf <file>    File containing contig name and orientation (+/-) delimited by a
                tab, one per line (optional; use this to define contigs that need
                to be reverse complemented)
  -h            help message (optional)

DESCRIPTION

This script takes as input an ace file and generates a file containing the information of the reads and it's mate. The format of the output file is as follows, where each item is separated by a tab:

  1.  read name
  2.  read start
  3.  read stop
  4.  read strand (+/-)
  5.  contig name of the read
  6.  contig length of the read
  7.  type of pairing (P-paired, U-unpaired, M-multiply placed)
  8.  read pair name
  9.  read pair start
  10. read pair stop
  11. read pair strand (+/-)
  12. contig name of the read pair 
  13. contig length of the read pair

VERSION

$Revision: 1.13 $

$Date: 2009-08-26 17:18:15 $

HISTORY