.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.12.
.TH TRANSIT-TPP "1" "August 2020" "transit-tpp 3.1.0" "User Commands"
.SH NAME
transit-tpp \- statistical calculations of essentiality of genes or genomic regions
.SH DESCRIPTION
usage: python PATH/src/tpp.py \fB\-bwa\fR <EXECUTABLE_WITH_PATH> \fB\-ref\fR <fasta\-file|comma_separated_list> \fB\-reads1\fR <FASTQ_OR_FASTA_FILE> [\-reads2 <FASTQ_OR_FASTA_FILE>] \fB\-output\fR <BASE_FILENAME> [OPTIONAL ARGS]
.IP
OPTIONAL ARGS:
.HP
\fB\-protocol\fR [Sassetti|Tn5|Mme1] # which sample prep protocol was used?; sassetti protocol is the default; this sets the default transposon and primer sequence
.TP
\fB\-primer\fR <seq>
# prefix of reads corresponding to end of transposon at junction with genomic sequence; can override default seq
.HP
\fB\-maxreads\fR <INT>
.TP
\fB\-mismatches\fR <INT>
# when searching for constant regions in reads 1 and 2; default is 1
.TP
\fB\-flags\fR "<STRING>"
# args to pass to BWA
.TP
\fB\-bwa\-alg\fR [aln|mem]
# Default: mem. Algorithm to use for mapping reads with bwa
.HP
\fB\-primer\-start\-window\fR INT,INT # position in read to search for start of primer; default is [0,20]
.TP
\fB\-window\-size\fR INT
# automatic method to set window
.HP
\fB\-barseq_catalog_in\fR|\-barseq_catalog_out <file>
.TP
\fB\-replicon\-ids\fR <comma_separated_list_of_names> # if multiple replicons/genomes/contigs/sequences were provided in \fB\-ref\fR, give them names.
# Enter 'auto' for autogenerated ids.