NAME

       transit-tpp - statistical calculations of essentiality of genes or genomic regions

DESCRIPTION

       usage:       python       PATH/src/tpp.py       -bwa      <EXECUTABLE_WITH_PATH>      -ref
       <fasta-file|comma_separated_list>       -reads1       <FASTQ_OR_FASTA_FILE>       [-reads2
       <FASTQ_OR_FASTA_FILE>] -output <BASE_FILENAME> [OPTIONAL ARGS]

              OPTIONAL ARGS:

       -protocol [Sassetti|Tn5|Mme1] # which sample prep protocol was used?; sassetti protocol is
              the default; this sets the default transposon and primer sequence

       -primer <seq>
              # prefix of reads corresponding to end  of  transposon  at  junction  with  genomic
              sequence; can override default seq

       -maxreads <INT>

       -mismatches <INT>
              # when searching for constant regions in reads 1 and 2; default is 1

       -flags "<STRING>"
              # args to pass to BWA

       -bwa-alg [aln|mem]
              # Default: mem. Algorithm to use for mapping reads with bwa

       -primer-start-window  INT,INT # position in read to search for start of primer; default is
              [0,20]

       -window-size INT
              # automatic method to set window

       -barseq_catalog_in|-barseq_catalog_out <file>

       -replicon-ids        <comma_separated_list_of_names>         #         if         multiple
       replicons/genomes/contigs/sequences were provided in -ref, give them names.
              # Enter 'auto' for autogenerated ids.