https://github.com/mbhall88/drprg

Drug Resistance Prediction with Reference Graphs
https://github.com/mbhall88/drprg

bioinformatics drug-resistance-prediction genome-graphs reference-graphs

Last synced: 2 months ago
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Drug Resistance Prediction with Reference Graphs

• Host: GitHub
• URL: https://github.com/mbhall88/drprg
• Owner: mbhall88
• License: mit
• Created: 2021-04-22T04:39:12.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2023-08-09T00:25:20.000Z (over 1 year ago)
• Last Synced: 2024-10-14T13:14:18.662Z (3 months ago)
• Topics: bioinformatics, drug-resistance-prediction, genome-graphs, reference-graphs
• Language: Rust
• Homepage: https://mbh.sh/drprg/
• Size: 18.1 MB
• Stars: 19
• Watchers: 8
• Forks: 1
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
👩‍⚕Dr. PRG - **D**rug **r**esistance **P**rediction with **R**eference **G**raphs️👨‍⚕️

[![codecov](https://codecov.io/gh/mbhall88/drprg/branch/main/graph/badge.svg?token=2WAA6MZRKK)](https://codecov.io/gh/mbhall88/drprg)

[![Rust](https://github.com/mbhall88/drprg/actions/workflows/rust.yml/badge.svg?branch=main)](https://github.com/mbhall88/drprg/actions/workflows/rust.yml)

[![github release version](https://img.shields.io/github/v/release/mbhall88/drprg)](https://github.com/mbhall88/drprg/releases)

[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

[![10.1099/mgen.0.001081](https://img.shields.io/badge/doi-10.1099%2Fmgen.0.001081-blue)](https://doi.org/10.1099/mgen.0.001081)

Full documentation: 

As the name suggests, Dr. PRG (pronounced "Doctor P-R-G") is a tool for predicting drug resistance from sequencing

data. It can be used for any species, provided an index is available for that species.

The [documentation][docs] outlines which species have prebuilt indices and also a guide

for how to create your own.

## Quick Installation

```

conda install -c bioconda drprg

```

Linux is currently the only supported platform; however, there is a Docker container that can be used on other platforms. 

See the [installation guide][install] for more options.

## Quick usage

Download the latest *M. tuberculosis* prebuilt index

```

drprg index --download mtb

```

Predict resistance from an Illumina fastq

```

drprg predict -x mtb -i reads.fq --illumina -o outdir/

```

### Help

```

$ drprg -h

Drug Resistance Prediction with Reference Graphs

Usage: drprg [OPTIONS] 

Commands:

  build    Build an index to predict resistance from

  predict  Predict drug resistance

  index    Download and interact with indices

  help     Print this message or the help of the given subcommand(s)

Options:

  -v, --verbose        Use verbose output

  -t, --threads   Maximum number of threads to use [default: 1]

  -h, --help           Print help (see more with '--help')

  -V, --version        Print version

```

## Citation

> Hall MB, Lima L, Coin LJM, Iqbal Z (2023) Drug resistance prediction for Mycobacterium tuberculosis with reference graphs. Microbial Genomics 9:001081. doi: [10.1099/mgen.0.001081](https://doi.org/10.1099/mgen.0.001081) 

```bib

@article{hall_drug_2023,

	title = {Drug resistance prediction for {Mycobacterium} tuberculosis with reference graphs},

	volume = {9},

	copyright = {All rights reserved},

	issn = {2057-5858},

	url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001081},

	doi = {10.1099/mgen.0.001081},

	number = {8},

	journal = {Microbial Genomics},

	author = {Hall, Michael B. and Lima, Leandro and Coin, Lachlan J. M. and Iqbal, Zamin},

	year = {2023},

	pages = {001081},

}

```

[docs]: https://mbh.sh/drprg/

[guide]: https://mbh.sh/drprg/guide/build/build.html

[install]: https://mbh.sh/drprg/installation.html