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iqbal-lab / Mykrobe-predictor

Antibiotic resistance predictions in minutes on a laptop
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We should document how to parallelise #99

Closed iqbal-lab closed 5 years ago

iqbal-lab commented 8 years ago

Just give a simple GNU parallels command people can copy.

RaSieb commented 7 years ago

Hi I've uploaded some scripts to use Mykrobe predictor staph and the "mykrobe genotype" on sets of illumina paired end reads to my GitHub: https://github.com/RaSieb/batchMykrobe. Required is an input directory containing sequence read files with _R1.fastq.gz and _R2.fastq.gz endings and for the genotype option a panel. The output is the .json files in the output directory, which can be coerced into a .tsv table with one line per sample with the additional python scripts.
Hopefully someone will find them useful. The scripts are written for mac.