---
name: "bacteria_tradis"
section: "1"
platform: "linux"
package: "bio-tradis"
version: "1.4.1+dfsg-1"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/bacteria_tradis"
---

# bacteria\_tradis(1)

bio-tradis: run a TraDIS analysis

## 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.