CAPYBARA

Capybara, a Core-snp Assignment PYthon tool for Acinetobacter baumannii

Capybara enables you to identify hierarchical populations in epidemic super-lineage (ESL) of Acinetobacter baumannii using a set of core-genome SNPs. For ESL or citation of Capybara, see DOI: 10.21203/rs.3.rs-4129268/v1.

Installation:

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

minimap2
mash
samtools
bcftools

You can easily install these packages using command below:

conda install -c bio-conda samtools bcftools minimap2 mash

Then you can use git to clone Capybara into your PC.

git clone git@github.com:Zhou-lab-SUDA/CAPYBARA.git

Quick Start (with examples)

$ cd /path/to/Capybara/

$ capy.py -i Examples/2.5.6.fna

It will generate a report file for Examples/2.5.6.fna about its population.

A single run for an assembled genome will finish <3 minutes for a 4 CPUs laptop (>10 minutes for short reads).

Usage

$ Usage: capy.py [OPTIONS]

Options:

  -i, --query TEXT  [Required] Input data, both assembled genome or short reads are acceptable.

  -p, --prefix TEXT [Optional] Prefix for output file. Default as Capy.

  -t, --threads INTEGER [Optional] Number of process to use. default: 8

  -l, --list TEXT   [Optional] A file containing list of query files, one per line.

  --help    Show this message and exit.

Capybara generates a report file in format below:

query	ESL	Lineage	Variant
2.5.6.fna	True	2.5	2.5.6
IC7.fna	False	-	-

Work flow and Reproduction Instructions

Work flow

A basic run for Capybara is as follows:

• ESL identification:
  • We pre-sketched all 5,824 representative genomes. Genetic distance between query data and pre-sketched data will be evaluated to find the most closed genomes.
  • If query data does not contains any sequential information related to ESL genomes, it will be classified as non-ESL. Otherwise, it will be analyzed as follows.
• Sequential alignment:
  • Query data will be aligned onto ESL's reference genome (MDR-TJ:GCF_000187205.2) to generate a BAM file.
• SNP calling:
  • A series SNPs will be called from BAM and then generate an VCF file.
• Population assignment:
  • Using a pre-built SNP scheme to assign hierarchical population of query data.

Workflow chart:

Reproduction Instructions

All data required for reproduction of the analysis were distributed in this repository under CAPYBARA/capydb/

which included:

• esl/esl.fna

Reference genome for ESL.

• msh/*.msh

5,824 pre-sketched files by Mash sketch.