drprg

Crates.io	drprg
lib.rs	drprg
version	0.1.1
source	src
created_at	2023-04-06 05:22:08.396419
updated_at	2023-04-06 05:40:57.75419
description	Drug resistance prediction with reference graphs
homepage	https://github.com/mbhall88/drprg
repository	https://github.com/mbhall88/drprg
max_upload_size
id	831940
size	5,468,214

Michael Hall (mbhall88)

documentation

README

👩‍⚕Dr. PRG - Drug resistance Prediction with Reference Graphs️👨‍⚕️

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 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...