Master :
Dev :
Installation
Python
(sudo) pip install git+https://github.com/Phelimb/atlas ## Required dependancy.
(sudo) pip install mykrobe
We recommend that you use a virtualenv to install mykrobe. If you haven't used virtualenv before please read a guide here.
Docker
docker run phelimb/mykrobe_predictor mykrobe --help
Usage
mykrobe predict --help
usage: mykrobe predict [-h] [-k kmer] [--tmp TMP]
[--skeleton_dir SKELETON_DIR]
[--mccortex31_path MCCORTEX31_PATH] [-q]
[--panel panel] [--force]
sample seq [seq ...] species
positional arguments:
sample sample id
seq sequence files (fastq or bam)
species species
optional arguments:
-h, --help show this help message and exit
-k kmer, --kmer kmer kmer length (default:21)
--tmp TMP tmp directory (default: /tmp/)
--skeleton_dir SKELETON_DIR
directory for skeleton binaries
--mccortex31_path MCCORTEX31_PATH (default:mccortex31)
Path to mccortex31
-q, --quiet do not output warnings to stderr
--panel panel variant panel (default:bradley-2015)
--force
AMR prediction
mykrobe predict tb_sample_id tb -1 tb_sequence.bam/fq
mykrobe predict staph_sample_id staph -1 staph_sequence.bam/fq
e.g.
mykrobe predict ERR117639 /download/ena/ERR117639*.gz tb
Output
Output is in JSON format. To convert to a less verbose tabular format use json_to_tsv.
{
"sample_id": {
"susceptibility": {
"Rifampicin": {
"predict": "S"
},
...
"Streptomycin": {
"predict": "S"
}
"phylogenetics": {
"lineage": {
"Unknown": {
"percent_coverage": -1,
"median_depth": -1
}
},
...
"species": {
"Mycobacterium_tuberculosis": {
"percent_coverage": 98.0,
"median_depth": 53
}
}
},
"typed_variants": {
"rpoB_N438S-AAC761118AGT": {
"info": {
"contamination_depths": [],
"coverage": {
"alternate": {
"percent_coverage": 47.62,
"median_depth": 0.0,
"min_depth": 47.0
},
"reference": {
"percent_coverage": 100.0,
"median_depth": 49.0,
"min_depth": 44.0
}
},
"expected_depths": [
56.0
]
},
"_cls": "Call.VariantCall",
"genotype": [
0,
0
],
"genotype_likelihoods": [
-4.25684443365591,
-99999999.0,
-99999999.0
]
}, ...
},
Change the panel for resistance prediction (TB only)
mykrobe predict tb_sample_id tb --panel walker-2015 -1 tb_sequence.bam
Walker, Timothy M., et al. "Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study." The Lancet Infectious Diseases 15.10 (2015): 1193-1202.
mykrobe predict tb_sample_id tb --panel bradley-2015 -1 tb_sequence.bam
Bradley, Phelim, et al. "Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis." Nature communications 6 (2015).
Choosing a panel for TB
In short, bradley-2015 is more specific, walker-2015 more sensitive. You can see a comparision of the results on ~3000 MTUB sequence here
Paper, citation
Please cite us if you use Mykrobe predictor in a publication
All analysis in this paper was done with release v0.1.3-beta.
Genotype on a catalog
mykrobe genotype [-h] [-k kmer] [--tmp TMP] [--keep_tmp]
[--skeleton_dir SKELETON_DIR]
[--mccortex31_path MCCORTEX31_PATH] [-t THREADS]
[--expected_depth EXPECTED_DEPTH] [-1 seq [seq ...]]
[-c ctx] [-f] [-q] [--ignore_filtered IGNORE_FILTERED]
sample probe_set
positional arguments:
sample sample id
probe_set probe_set
optional arguments:
-h, --help show this help message and exit
-1 seq [seq ...], --seq seq [seq ...]
sequence files (fasta,fastq,bam)
-c ctx, --ctx ctx cortex graph binary
-k kmer, --kmer kmer kmer length (default:21)
--tmp TMP tmp directory (default: /tmp/)
--keep_tmp Dont remove tmp files
--skeleton_dir SKELETON_DIR
directory for skeleton binaries
--mccortex31_path MCCORTEX31_PATH
Path to mccortex31
-t THREADS, --threads THREADS
threads
--expected_depth EXPECTED_DEPTH
expected depth
-f, --force force
-q, --quiet do not output warnings to stderr
e.g.
head example-data/staph-amr-bradley_2015.fasta
>mecA?name=mecA&version=1
ATGAATATAGTTGAAAATGAAATATGTATAAGA...ATAAAAGGACTTATAAAGATTGA
>mecA?name=mecA&version=2
ATGAATATAGTTGAAAATGAAATATGTATAAGA...TGAAGATTTGCCAGAACATGAAT
>fusA?name=fusA&version=1
ATGAATATAGTTGAAAATGAAATATGTATAAGA...TGAAGATTTGCCAGAACATGAAT
mykrobe genotype sample_id example-data/staph-amr-bradley_2015.fasta -1 seq.fq
{
"sample_id": {
"files": [
"seq.fq "
],
"kmer": 21,
"sequence_calls": {
"mecA": {
"info": {
"copy_number": 0.0,
"contamination_depths": [],
"coverage": {
"percent_coverage": 0.0,
"median_depth": 0.0,
"min_non_zero_depth": 0.0
},
"expected_depths": [
1
]
},
"_cls": "Call.SequenceCall",
"genotype": [
0,
0
],
"genotype_likelihoods": [
-0.001,
-99999999.0,
-99999999.0
]
},
"fusA": {
"info": {
"copy_number": 1.0276923076923077,
"contamination_depths": [],
"version": "10",
"coverage": {
"percent_coverage": 100.0,
"median_depth": 167.0,
"min_non_zero_depth": 116.0
},
"expected_depths": [
162.5
]
},
"_cls": "Call.SequenceCall",
"genotype": [
1,
1
],
"genotype_likelihoods": [
-994.7978064088725,
-349.45246450237215,
-10.95808091830304
]
},
....
}
}
Comparing results
./scripts/compare.py
usage: compare.py [-h] [--analysis {summary,table,diff}]
[--ana1 ANA1 [ANA1 ...]] [--ana2 ANA2 [ANA2 ...]]
[--format {short,long}]
truth
e.g. Get a summary of a commit vs the truth.
Truth JSON is in the form:
{
"TRL0079551-S12": {
"susceptibility": {
"Rifampicin": {
"predict": "S"
},
"Capreomycin": {
"predict": "S"
},
...
"Quinolones": {
"predict": "S"
}
}
},
}
compare.py --analysis summary truth.json --ana1 *.json
Output
Ana1
Drug Total FN(R) FP(S) VME ME sensitivity specificity PPV NPV
Rifampicin 99 1 (24) 1 (75) 4.2% 1.3% 95.8% 98.7% 95.8% 98.7%
Capreomycin 14 0 (4) 0 (10) 0.0% 0.0% 100.0% 100.0% 100.0% 100.0%
all 539 23 (128) 14 (411) 18.0% 3.4% 82.0% 96.6% 88.2% 94.5%
...
Other options for --analysis are diff and table which will report a table showing samples where two analyses differed and a full table of comparisions respectively.
e.g.
sample drug truth ana1 ana2
10205-03 Quinolones NA R S
10091-01 Isoniazid S R S
Common issues
- mccortex install fails
mccortex should be installed automatically with the atlas dependancy. If for some reason it doesn't you can run a manual install:
git clone --recursive https://github.com/iqbal-lab/Mykrobe-predictor.git
cd Mykrobe-predictor
cd mccortex
make
export PATH=$PATH:$(pwd)/bin
cd ..
