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mutAMR was designed to be a simple to install and use tool for identification of variants for use in detecting variant based AMR mechanisms. It simply creates an annotated vcf file for use as input to tools for reporting AMR. In particular, for M. tuberculosis, but any species will work if you have reference file then you have enough to generate a vcf.

There are many high quality tools that also do this. However, many are part of much larger pipelines or workflows that were not required for the need that mutAMR was designed to address. Specifically, in a clinical and public health laboratory (CPHL), bioinformatics tools are often required to fit into larger processes and large pipelines are difficult to implement in this setting.

What is mutAMR NOT?

mutAMR is NOT a

• Pipeline to provide hands off interpretations for AMR. If you require a tool like that - please use mykrobe or TB-Profiler
• Tool designed for generation of alignments suitable for phylogenetic or core-genome analysis. If you require a tool like this - please use snippy

Dependencies

mutAMR is a python package that runs

• bwa-mem to align reads to reference genome
• freebayes to identify variants. Note variants will be identified down to the minimum fraction designated by the user (default 0.1), see Running mutAMR.
• If installed, delly will be used to identify large deletions. If not installed - then small deletions will be reported as detected by freebayes. A combined vcf file will be generated, combining the variants detected by freebayes and delly.
• Annotation will be undertaken using snpEff, to allow for simple integration with the WHO M. tuberculosis catalogue V2.