👩⚕Dr. PRG - Drug resistance Prediction with Reference Graphs️👨⚕️
Full documentation: https://mbh.sh/drprg/
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 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 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] <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
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
@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},
}