This is based on a modified version of the JGI microbial isolate pipeline, removing the steps related to collecting metrics and evaluating the generated assembly. The pipeline was developed at the JGI and is based around preprocessing then assembly of overlapping 2x150bp reads from Illumina HiSeq 2500.
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Normalisation is not included in the pipeline as it not recommended for isolate data, though it may be beneficial for metagenome, single cell or RNA-seq data.
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The JGI decontamination steps are not included here. These include removing any reads matching to common animal contaminants (human, cat, dog, mouse) and common microbial contaminants (E.coli, Pseudomonas sp., Delftia sp, others).