NAME

       bacteria_tradis - bio-tradis: run a TraDIS analysis

SYNOPSIS

       bacteria_tradis [options]

DESCRIPTION

       Run a TraDIS analysis. This involves: 1: filtering the data with tags matching that passed
       via -t option 2: removing the tags from the sequences 3: mapping 4: creating an  insertion
       site plot 5: creating a stats summary

OPTIONS

       -f     text file listing fastq files with tradis tags attached

       -t     tag to search for

       -r     reference genome in fasta format (.fa)

       -td    tag direction - 3 or 5 (optional. default = 3)

       -mm    number of mismatches allowed when matching tag (optional. default = 0)

       -m     mapping quality cutoff score (optional. default = 30)

       --smalt_k
              custom k-mer value for SMALT mapping (optional)

       --smalt_s
              custom step size for SMALT mapping (optional)

       --smalt_y
              custom y parameter for SMALT (optional. default = 0.96)

       --smalt_r
              custom r parameter for SMALT (optional. default = -1)

       -n     number of threads to use for SMALT and samtools sort (optional. default = 1)

       -e     set defaults for essentiality experiment (smalt_r = 0, -m = 0)

       -v     verbose debugging output

AUTHOR

       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.