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:

```bash

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:

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

Get RDscan snakemake workflow:

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

Install all required dependencies:

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

Usage

Activate RDscan environment:

bash conda activate RDscan

Run pipeline:

bash 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:

bash 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 | | --------- | ------ | ------ | ---- | --- | ---- | --------- | --------- | --------- | --------- | | NC000962 | 333828 | 338580 | 5800 | | DEL | 7113 | 7084 | 7050 | | NC000962 | 340400 | 340645 | 245 | | DEL | | | | | | NC000962 | 350935 | 351175 | 238 | | DEL | | 300 | 204 | 240 | | NC000962 | 361769 | 362988 | 1391 | | DEL | 1833 | 1392 | 1833 | 1390 |

Example of the RD_known.tsv:

Table containing proportion of coverage in particular RDs.

| Sample | N-RD25tbA | N-RD25tbB | 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-RD25tbA | N-RD25tbB | 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