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NAME

TraFiC_candReads.pl - Find candidate reads for transposon or viral detection

SYNOPSIS

TraFiC_candReads.pl [-h] -o /some/path/ -i sample.bam -i lane.ump.bam ...

  Required options:

    --input   (-i)  Define at least once

  Other options:

    --output  (-o)  Output written to specified folder as candidates.fa [.]

    --chr     (-c)  Process just this chromosome/contig
                     - Output will be prefixed with seq name
                     - Additional output files of <chr>.o1.fa and <chr>.o2.fa generated
                        - handling these is out of the scope of this help.

    --help    (-h)  This message

  Examples:
    TraFiC_candReads.pl -o $HOME/trafic/COLO-829 -i COLO-829.bam

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