Assemble bacterial isolate genomes from Illumina paired-end reads

 Shovill is a pipeline which uses SPAdes at its core,
 but alters the steps before and after the primary
 assembly step to get similar results in less time.
 Shovill also supports other assemblers like SKESA,
 Velvet and Megahit, so you can take advantage of the
 pre- and post-processing the Shovill provides
 with those too.