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

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Full documentation: <https://mbh.sh/drprg/>

As the name suggests, DrPRG 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 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] <COMMAND>

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 <INT>  Maximum number of threads to use [default: 1]
  -h, --help           Print help (see more with '--help')
  -V, --version        Print version
```

## Citation

Preprint coming soon...

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

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