CroTrait:
A portable tool for in silico species identification, O serotyping and multilocus sequence typing of Cronobacter genus

Introduction

This is the homepage of CroTrait, a software package that performs efficient inference of species, O serotypes and STs of Cronobacter. CroTrait was developed by Lu Wang. CroTrait is called from a directory containing one or multiple genome sequences and each genome sequence should be saved to a separate file in FASTA format. Input files can either be complete genomes or draft genomes. It is able to analyze hundreds of genomes data in a matter of hours on an ordinary PC. Moreover, post data analysis and visualization module embedded in CroTrait further assist the user in checking and analyzing the data.

if you use this software package please cite:
Lu Wang, et al. In silico species identification and serotyping for Cronobacter isolates by use of whole-genome sequencing data [J]. International Journal of Food Microbiology, 2021, 358: 109405.

Environment set up

CroTrait is a program written in python and the external software BLAST+ and MEGA need to be installed and configured locally:

python (version 3.8.0)

dependencies
biopython (version 1.78 or higher)
numpy
matplotlib
pandas

MEGA (version X (64-bit))

BLAST+ (version 2.9.0)

User guide

1. identify species, O serotypes and STs

1.1. Assemblies with unknown species
$CroTrait -d directory [-p prefix]
-p: represent the prefix of result file

1.2. Assemblies with known species (one of the seven species of Cronobacter)
$CroTrait -d directory -s species [-p prefix]

2. generate O antigen clusters (O-AGCs) pattern

$CroTrait -t 2 -d genomes -s species
example figure

3. extract O-AGCs sequences in batch format

$CroTrait -t 3 -d directory [-p prefix]

4. post statistics analysis

$CroTrait -t 4 -r result_table
-r: the result created by "1", namely table with identified species and O serotypes.
after executing this command, 6 table will generated according to the species and O serotypes.

5. post visulization analysis

example figure

License

CroTrait is a free software package, licensed under MIT.

Feedback/Issues

If you need assistance using CroTrait, you can get in touch by emailing Lu Wang ([email protected]), or by asking on Issues page.