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drprg
Young edited this page Feb 14, 2024
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Dr PRG
Dr. PRG - Drug resistance Prediction with Reference Graphs️
About : |
As the name suggests, Dr. PRG (pronounced "Doctor P-R-G") is a tool for predicting drug resistance from sequencing data.
Grandeur only uses Dr. PRG for TB antibiotic susceptible/resistant profiles.
Documentation : https://github.com/mbhall88/drprg
Citation : https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001081
Directory tree:
drprg/
├── drprg_summary.tsv
├── sample
│ ├── discover
│ │ ├── denovo_paths.txt
│ │ ├── denovo_sequences.fa
│ │ ├── discover.log
│ │ └── sample
│ │ ├── denovo_paths.txt
│ │ ├── denovo_sequences.fa
│ │ ├── sample.filtered.sam
│ │ ├── pandora.consensus.fq.gz
│ │ └── pandora.pangraph.gfa
│ ├── kmer_covgs.txt
│ ├── kmer_probs.txt
│ ├── sample.drprg.bcf
│ ├── sample.drprg.json
│ ├── sample.filtered.sam
│ ├── pandora.consensus.fq.gz
│ ├── pandora_consensus.vcf
│ ├── pandora_genotyped.vcf
│ ├── pandora.log
│ └── pandora.pangraph.gfa
└── sample_drprg.tsv
Example file for an individual sample (sample.drprg.json)
{
"genes": {
"absent": [],
"present": [
"ahpC",
"ddn",
"eis",
"embA",
"embB",
"ethA",
"fabG1",
"gid",
"gyrA",
"gyrB",
"inhA",
"katG",
"pncA",
"rplC",
"rpoB",
"rpsL",
"rrs",
"tlyA"
]
},
"sample": "myco_GCF_000195955.2",
"susceptibility": {
"Amikacin": {
"evidence": [
{
"gene": "eis",
"residue": "DNA",
"variant": "C-14T",
"vcfid": "e64f7e27"
},
{
"gene": "rrs",
"residue": "DNA",
"variant": "G1484X",
"vcfid": "9049e055"
}
],
"predict": "F"
},
"Capreomycin": {
"evidence": [
{
"gene": "rrs",
"residue": "DNA",
"variant": "G1484X",
"vcfid": "9049e055"
}
],
"predict": "F"
},
"Ciprofloxacin": {
"evidence": [
{
"gene": "gyrA",
"residue": "PROT",
"variant": "G88A",
"vcfid": "e1c2ee47"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "G88C",
"vcfid": "e1c2ee47"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "S91P",
"vcfid": "50c740bf"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "A90V",
"vcfid": "50c740bf"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94N",
"vcfid": "9dbd1282"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94Y",
"vcfid": "9dbd1282"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94G",
"vcfid": "9dbd1282"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94H",
"vcfid": "9dbd1282"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94A",
"vcfid": "9dbd1282"
}
],
"predict": "F"
},
"Delamanid": {
"evidence": [],
"predict": "S"
},
"Ethambutol": {
"evidence": [
{
"gene": "embA",
"residue": "DNA",
"variant": "C-16T",
"vcfid": "d2217772"
},
{
"gene": "embA",
"residue": "DNA",
"variant": "C-16G",
"vcfid": "d2217772"
},
{
"gene": "embA",
"residue": "DNA",
"variant": "C-12T",
"vcfid": "d2217772"
}
],
"predict": "F"
},
"Ethionamide": {
"evidence": [],
"predict": "S"
},
"Isoniazid": {
"evidence": [
{
"gene": "ahpC",
"residue": "DNA",
"variant": "C-72T",
"vcfid": "c3e661f6"
},
{
"gene": "inhA",
"residue": "PROT",
"variant": "I194T",
"vcfid": "5330b912"
}
],
"predict": "F"
},
"Kanamycin": {
"evidence": [
{
"gene": "eis",
"residue": "DNA",
"variant": "C-12T",
"vcfid": "e64f7e27"
},
{
"gene": "eis",
"residue": "DNA",
"variant": "G-10A",
"vcfid": "e64f7e27"
},
{
"gene": "eis",
"residue": "DNA",
"variant": "C-14T",
"vcfid": "e64f7e27"
},
{
"gene": "rrs",
"residue": "DNA",
"variant": "G1484X",
"vcfid": "9049e055"
}
],
"predict": "F"
},
"Levofloxacin": {
"evidence": [
{
"gene": "gyrA",
"residue": "PROT",
"variant": "G88A",
"vcfid": "e1c2ee47"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "G88C",
"vcfid": "e1c2ee47"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "S91P",
"vcfid": "50c740bf"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "A90V",
"vcfid": "50c740bf"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94N",
"vcfid": "9dbd1282"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94Y",
"vcfid": "9dbd1282"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94G",
"vcfid": "9dbd1282"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94H",
"vcfid": "9dbd1282"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94A",
"vcfid": "9dbd1282"
}
],
"predict": "F"
},
"Linezolid": {
"evidence": [
{
"gene": "rplC",
"residue": "PROT",
"variant": "C154R",
"vcfid": "ac3cfc1b"
}
],
"predict": "F"
},
"Moxifloxacin": {
"evidence": [
{
"gene": "gyrA",
"residue": "PROT",
"variant": "G88A",
"vcfid": "e1c2ee47"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "G88C",
"vcfid": "e1c2ee47"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "S91P",
"vcfid": "50c740bf"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "A90V",
"vcfid": "50c740bf"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94N",
"vcfid": "9dbd1282"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94Y",
"vcfid": "9dbd1282"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94G",
"vcfid": "9dbd1282"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94H",
"vcfid": "9dbd1282"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94A",
"vcfid": "9dbd1282"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94C",
"vcfid": "9dbd1282"
}
],
"predict": "F"
},
"Ofloxacin": {
"evidence": [
{
"gene": "gyrA",
"residue": "PROT",
"variant": "G88A",
"vcfid": "e1c2ee47"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "G88C",
"vcfid": "e1c2ee47"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "G88N",
"vcfid": "e1c2ee47"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "S91P",
"vcfid": "50c740bf"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "A90V",
"vcfid": "50c740bf"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94N",
"vcfid": "9dbd1282"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94Y",
"vcfid": "9dbd1282"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94G",
"vcfid": "9dbd1282"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94H",
"vcfid": "9dbd1282"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94A",
"vcfid": "9dbd1282"
},
{
"gene": "gyrA",
"residue": "PROT",
"variant": "D94C",
"vcfid": "9dbd1282"
}
],
"predict": "F"
},
"Pyrazinamide": {
"evidence": [
{
"gene": "pncA",
"residue": "PROT",
"variant": "D49Y",
"vcfid": "0a83770f"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "D49H",
"vcfid": "0a83770f"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "D49E",
"vcfid": "0a83770f"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "H51L",
"vcfid": "0a83770f"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "H51Y",
"vcfid": "0a83770f"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "H51N",
"vcfid": "0a83770f"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "H51P",
"vcfid": "0a83770f"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "D49A",
"vcfid": "0a83770f"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "H51R",
"vcfid": "0a83770f"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "H51D",
"vcfid": "0a83770f"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "D49G",
"vcfid": "0a83770f"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "TTC148TTT",
"vcfid": "0a83770f"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "H51Q",
"vcfid": "0a83770f"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "D49N",
"vcfid": "0a83770f"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "D49V",
"vcfid": "0a83770f"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "H57Q",
"vcfid": "541508c6"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "H57L",
"vcfid": "541508c6"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "F58I",
"vcfid": "541508c6"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "H57Y",
"vcfid": "541508c6"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "CGGGTGACCA161A",
"vcfid": "541508c6"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "H57N",
"vcfid": "541508c6"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "H57D",
"vcfid": "541508c6"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "F58S",
"vcfid": "541508c6"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "H57R",
"vcfid": "541508c6"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "F58L",
"vcfid": "541508c6"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "H57P",
"vcfid": "541508c6"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "P62R",
"vcfid": "54447e1e"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "CCG184CCC",
"vcfid": "54447e1e"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "P62S",
"vcfid": "54447e1e"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "P62T",
"vcfid": "54447e1e"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "P62Q",
"vcfid": "54447e1e"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "P62L",
"vcfid": "54447e1e"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "C185CGGACTATTC",
"vcfid": "54447e1e"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "P62A",
"vcfid": "54447e1e"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "CCG184CCA",
"vcfid": "54447e1e"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "CGGCACACCGGACTATTCCTCGTCG177ACCGGACTATTCCTCGTCG",
"vcfid": "54447e1e"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "CCG184CCT",
"vcfid": "54447e1e"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "CGGCACACCGGACTATTCCTCGTCG177ACCGGACTATTCCTCGTCG",
"vcfid": "19ad43e1"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "P69Q",
"vcfid": "19ad43e1"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "W68G",
"vcfid": "19ad43e1"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "W68L",
"vcfid": "19ad43e1"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "TCG199TAA",
"vcfid": "19ad43e1"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "S67P",
"vcfid": "19ad43e1"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "TCG199TAG",
"vcfid": "19ad43e1"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "TGG202TGA",
"vcfid": "19ad43e1"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "W68R",
"vcfid": "19ad43e1"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "W68C",
"vcfid": "19ad43e1"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "P69L",
"vcfid": "19ad43e1"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "TGG202TAA",
"vcfid": "19ad43e1"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "ACTATTCCTCGTCG188AG",
"vcfid": "19ad43e1"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "TGG202TAG",
"vcfid": "19ad43e1"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "TCG199TGA",
"vcfid": "19ad43e1"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "T76S",
"vcfid": "79f0cd6a"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "AGCGGTACTCCCG220G",
"vcfid": "79f0cd6a"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "T76P",
"vcfid": "79f0cd6a"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "T76I",
"vcfid": "79f0cd6a"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "TGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTAT359TGCGGCAACGCGGCGTCGATGAGGTCGGTAT",
"vcfid": "9a1a029b"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "GTC373GTA",
"vcfid": "9a1a029b"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "GTC373GTG",
"vcfid": "9a1a029b"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "V125G",
"vcfid": "9a1a029b"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "TGCGGCAACGCGGCGTCGATGAGGTCGATGTGGTCGGTAT359TGCGGCAACGCGGCGTGGTCGGTAT",
"vcfid": "9a1a029b"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "V125A",
"vcfid": "9a1a029b"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "GTC373GTT",
"vcfid": "9a1a029b"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "V125F",
"vcfid": "9a1a029b"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "CAG421TAG",
"vcfid": "2183643d"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "ACG424ACA",
"vcfid": "2183643d"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "Q141P",
"vcfid": "2183643d"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "ACG424ACC",
"vcfid": "2183643d"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "T142R",
"vcfid": "2183643d"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "CAG421TAA",
"vcfid": "2183643d"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "ACG424ACT",
"vcfid": "2183643d"
},
{
"gene": "pncA",
"residue": "DNA",
"variant": "CAG421TGA",
"vcfid": "2183643d"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "T142K",
"vcfid": "2183643d"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "T142A",
"vcfid": "2183643d"
},
{
"gene": "pncA",
"residue": "PROT",
"variant": "T142M",
"vcfid": "2183643d"
}
],
"predict": "F"
},
"Rifampicin": {
"evidence": [
{
"gene": "rpoB",
"residue": "PROT",
"variant": "V170F",
"vcfid": "33ebe38d"
},
{
"gene": "rpoB",
"residue": "DNA",
"variant": "GACCAGAACAACCCGCTGTCGGGGTTGACCCACA1303GCCCAGAACAACCCGCTGTCCGGGCCCC",
"vcfid": "4020ad9c"
},
{
"gene": "rpoB",
"residue": "DNA",
"variant": "CCCACAAG1331CC",
"vcfid": "3759d176"
},
{
"gene": "rpoB",
"residue": "DNA",
"variant": "TTGACCCACAA1327TGGCCCCA",
"vcfid": "3759d176"
},
{
"gene": "rpoB",
"residue": "DNA",
"variant": "TGACCCACAA1328GGCCCCA",
"vcfid": "3759d176"
},
{
"gene": "rpoB",
"residue": "DNA",
"variant": "GACCAGAACAACCCGCTGTCGGGGTTGACCCACA1303GCCCAGAACAACCCGCTGTCCGGGCCCC",
"vcfid": "3759d176"
},
{
"gene": "rpoB",
"residue": "DNA",
"variant": "ACTGTCGGCG1344A",
"vcfid": "9fdf7754"
}
],
"predict": "F"
},
"Streptomycin": {
"evidence": [
{
"gene": "gid",
"residue": "DNA",
"variant": "ATATCGGTAGCGGAGC200C",
"vcfid": "290d169a"
},
{
"gene": "gid",
"residue": "DNA",
"variant": "ATATCGGTAGCGGAGCC200CC",
"vcfid": "290d169a"
}
],
"predict": "F"
}
},
"version": {
"drprg": "0.1.1",
"index": "20230308"
}
}
Example file for run (drprg/drprg_summary.tsv)
sample genes_present genes_absent susceptibility
myco_GCF_000195955.2 ahpC,ddn,eis,embA,embB,ethA,fabG1,gid,gyrA,gyrB,inhA,katG,pncA,rplC,rpoB,rpsL,rrs,tlyA Amikacin,Capreomycin,Ciprofloxacin,Delamanid,Ethambutol,Ethionamide,Isoniazid,Kanamycin,Levofloxacin,Linezolid,Moxifloxacin,Ofloxacin,Pyrazinamide,Rifampicin,Streptomycin
-
- amrfinderplus
- bbduk
- blastn
- blobtools_*
- core_genome_evaluation
- circulocov
- datasets_*
- drprg
- elgato
- emmtyper
- fastani
- fastp
- fastqc
- heatcluster
- iqtree2
- kaptive
- kleborate
- kraken2
- mash_*
- mashtree
- mlst
- multiqc
- mykrobe
- panaroo
- pbptyper
- phytreeviz
- plasmidfinder
- prokka
- quast
- seqsero2
- serotypefinder
- shigatyper
- snp_dists
- spades