| The SPAdes genome assembler has become the de facto standard de novo genome assembler for Illumina whole genome sequencing data of bacteria and other small microbes. SPAdes was a major improvement over previous assemblers like Velvet, but it can be very slow to run and does not handle overlapping paired-end reads well. Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get near-identical results in far less time. |
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/shovill