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.

transit-tpp 3.1.0                                  August 2020                                    TRANSIT-TPP(1)