VibcSNP

SNP barcode decoding program for Vibrio cholerae

Installation

VibcSNP spell was devoloped and tested in Python 3.9.0, and requires a several modules:

fastANI
samtools
bcftools
minimap2

Enjoy a cup of coffee while installing these packages using commands below:

pip install fastani minimap2
conda install -c bio-conda samtools bcftools minimap2
FYI: some version of pandas might not be support DataFrame.append() any more.

Quick Start (with example)

VibcSNP requires a sequence file(in fasta format), you can simply submit your genome following -q/--query flag:

python  VibcSNP.py -q vc_example[you can replace it with your own genome]

The first step of VibcSNP is to check the species of the genome using 95 of average nucleotide identity against the reference genome of Vibrio cholerae N16961.

If average nucleotide identity is lower than threshold, VibcSNP will exit.

Try a non-Vibrio cholerae genome with command below:
python  VibcSNP.py -q non_vc_example

If genome is likely to be Vibrio cholerae, VibcSNP will print the value of average nucleotide identity.

The second step of VibcSNP is to detect a series of specific SNPs from monophyletic groups we have identified.

python  VibcSNP.py -q vc_example

Command above will print such information:

yyyy-mm-dd time ---Species Identification---

yyyy-mm-dd time Input genome is from species vibrio cholerae

yyyy-mm-dd time Average Nucleotide Identity: 98.1241

yyyy-mm-dd time ---SNP detection---

yyyy-mm-dd time SNP lineage: 3.4.8

yyyy-mm-dd time ---Done---