CampyCPS

CampyCPS is a tool for Campylobacter CPS relevant genes identification.

usage: CampyCPS -i <genome assemble directory> -o <output_directory>

Author: Qingpo Cui(SZQ Lab, China Agricultural University)

optional arguments:
  -h, --help      show this help message and exit
  -i I            <input_path>: the PATH to the directory of assembled genome files. Could not use with -f
  -f F            <input_file>: the PATH of assembled genome file. Could not use with -i
  -o O            <output_directory>: output PATH
  -minid MINID    <minimum threshold of identity>, default=95
  -mincov MINCOV  <minimum threshold of coverage>, default=90
  -init      <initialize the reference database>
  -t T            <number of threads>: default=8
  -v, --version   Display version

Installation

Using pip

pip3 install CampyCPS

Using conda

comming soon...

Dependency

• BLAST+ >2.7.0

you should add BLAST in your PATH

Blast installation

Windows

Following this tutorial: Add blast into your windows PATH

Linux/Mac

The easyest way to install blast is:

conda install -c bioconda blast

Usage

The first time when running CampyCPS, you should use CampyCPS -init command to initialize your database.

The default database including the following genes.

CPS relevant genes

Example

# Single Genome Mode
CampyCPS -f /PATH_TO_ASSEBLED_GENOME/sample.fa -o PATH_TO_OUTPUT

# Batch Mode
CampyCPS -i /PATH_TO_ASSEBLED_GENOME_DIR -o PATH_TO_OUTPUT