pipeline for MTBC putative regions of difference discovery

• pipeline for MTBC putative regions of difference discovery
  • Description
  • Installation
  • Usage
  • Output
  • Citation
  • License

Description

RDscan is a snakemake workflow to find deletions and putative regions of difference (RDs) in mycobacterium tuberculosis complex (MTBC) genomes, it is also capable to determine already known or user defined RDs.

Installation

The usage of this workflow is described in the Snakemake Workflow Catalog, alternatively it can be installed as described below.

Use the Conda package manager and BioConda channel to install RDscan.

If you do not have conda installed do the following:

# Download Conda installer
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
# Set permissions
chmod -X Miniconda3-latest-Linux-x86_64.sh
# Install
bash Miniconda3-latest-Linux-x86_64.sh

Set up channels:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Get RDscan snakemake workflow:

git clone https://github.com/dbespiatykh/RDscan.git

Install all required dependencies:

cd RDscan
conda install -c conda-forge mamba
mamba env create --file environment.yml

Usage

Rulegraph of the pipeline

Activate RDscan environment:

conda activate RDscan

Run pipeline:

snakemake --conda-frontend mamba --use-conda -j {Number of cores}

It is recommended to use dry run if you are running pipeline for the first time, to see if everything is in working order, for this you can use -n flag:

snakemake -n

Output

Output in the results directory will contain four tables: RD_putative.tsv, RD_known.tsv, RD_known.xlsx, and RD_known.bin.tsv

Example of the RD_putative.tsv: Table containing all discovered putative RDs.

RD - Known RDs that intersects with deletion breakpoints; SIZE - Estimated size of predicted deletion.

Values in cells represent deletion length in the sample.

CHROM	START	END	SIZE	RD	TYPE	ERR015582	ERR017778	ERR017782	ERR019852
NC_000962	333828	338580	5800		DEL	7113	7084	7050
NC_000962	340400	340645	245		DEL
NC_000962	350935	351175	238		DEL		300	204	240
NC_000962	361769	362988	1391		DEL	1833	1392	1833	1390

Example of the RD_known.tsv:

Table containing proportion of coverage in particular RDs.

Sample	N-RD25_tbA	N-RD25_tbB	N-RD25bov/cap	N-RD25das
ERR015582	0.883562	0.856164	0.856164	0.808219
ERR017778	0	0	0	0.41791
ERR017782	1.021277	1.042553	1.106383	0.978723
ERR019852	0	0	0	0.386364

Example of the RD_known.xlsx:

Same as the RD_known.tsv, but in a XLSX format with applied contiditional formatting.
Conditional formatting corresponds with threshold value in a config.yml file.

Binary version of the RD_known.bin.tsv:

Sample	N-RD25_tbA	N-RD25_tbB	N-RD25bov/cap	N-RD25das
ERR015582	0	0	0	0
ERR017778	1	1	1	0
ERR017782	0	0	0	0
ERR019852	1	1	1	0

Citation

If you use RDscan for your research, please cite the pipeline:

D. Bespiatykh, J. Bespyatykh, I. Mokrousov, and E. Shitikov, A Comprehensive Map of Mycobacterium tuberculosis Complex Regions of Difference, mSphere, Volume 6, Issue 4, 21 July 2021, Page e00535-21, https://doi.org/10.1128/mSphere.00535-21

All references for the tools utilized by the RDscan can be found in the CITATIONS.md file.

License

MIT