Mykrobe predictor protocols

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Mykrobe predictor statistics

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Mykrobe predictor specifications

Information


Unique identifier OMICS_08316
Name Mykrobe predictor
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Oxford Nanopore
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Bacteria
    • Staphylococcus aureus

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Documentation


Publication for Mykrobe predictor

Mykrobe predictor in pipelines

 (2)
2018
PMCID: 5933776
PMID: 29723202
DOI: 10.1371/journal.pone.0195860

[…] notably from both the mlst 5 and mlst 8 strains (). antibiotic susceptibility profiles of each b0 isolate and the earliest nasal isolate from each subject were inferred in silico and compared using mykrobe predictor analysis []. no differences were observed in the predicted antibiotic susceptibility profiles between pairs of isolates from each subject (data not shown). comparison […]

2017
PMCID: 5405248
PMID: 28275074
DOI: 10.1128/JCM.02483-16

[…] of >100). figures s6 and s7 show the genotype confidence distribution split by whether the genotype is correct or not., yield and timing were analyzed with poretools (). for the r9.4 sample, mykrobe predictor was applied to the cumulative read output at each hour. the yield of bcg was measured by mapping to a bcg reference (accession no. bx248333.1)., phylogenetic placement of the 15% […]


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Mykrobe predictor in publications

 (8)
PMCID: 5933776
PMID: 29723202
DOI: 10.1371/journal.pone.0195860

[…] were made by searching each set of contigs for sequences of the housekeeping genes (arcc, aroe, glpf, gmk, pta, tpi, yqil) and comparing these to a database of s. aureus types for mlst []. mykrobe predictor was used to predict the antibiotic resistant profiles from the a5 pipeline results []., to infer the evolutionary relationships among the s. aureus isolates, sequence reads […]

PMCID: 5882078
PMID: 29458686
DOI: 10.1099/jmm.0.000664

[…] the top species hits from kraken (for s. aureus genbank bx571856.1 and for e. coli genbank ae014075.1). for staphylococcus sp. specimens, the species was also predicted via the publically available mykrobe predictor []. mykrobe also predicts antibiotic susceptibility for s. aureus (mykrobe v0.3.6–0-g9d196c7), while antibiotic susceptibility for e. coli and klebsiella sp. was predicted using […]

PMCID: 5628838
PMID: 28982116
DOI: 10.1371/journal.pone.0185656

[…] were manually inspected for variants occurring in amr genes listed in the tbdream database []. samples in which there was potential evidence of amr-loci via this analysis were also run through mykrobe predictor-tb [] in order to confirm associations., raw fastq sequence data was obtained from ncbis sequence read archive (sra), from three canadian wgs studies of endemic canadian tb […]

PMCID: 5405248
PMID: 28275074
DOI: 10.1128/JCM.02483-16

[…] of greater genome-wide diversity in direct samples (see fig. s1 in the supplemental material)., all sequenced culture-positive (37/39) direct m. tuberculosis samples were successfully identified by mykrobe predictor to complex level (37/37) and 95% to species level (35/37), including 13/37 (35%) where the mean depth of coverage was <3×. all mgit cultures were identified as m. tuberculosis. […]

PMCID: 5376617
PMID: 28421046
DOI: 10.3389/fmicb.2017.00543

[…] reference for vwbp seq1 was obtained from s. aureus dl584 (hm228920); and reference for lukp and lukq were obtained from s. aureus 3711 (lt671578). genotypic resistance profiles were obtained with mykrobe predictor v0.4.3 build 0-gd6c8714 (bradley et al., )., occurrence of total mrsa, mrsa cc398, and mrsa cc398 t034 (the only mrsa type of this study associated to pigs) were analyzed […]


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