---
name: "transit-tpp"
section: "1"
platform: "linux"
package: "tnseq-transit"
version: "3.3.12-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/transit-tpp"
---

# transit-tpp(1)

statistical calculations of essentiality of genes or genomic regions

## 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.