A5-miseq

A5-miseq is an open-source tool for de novo genome assembly of microbial genomes from Illumina data, which can automate all steps of the process without the need for parameter tuning. It can trim adapters, filter quality, correct errors, generate contigs and scaffolds, and detect misassemblies. A5-miseq uses long reads from the Illumina MiSeq and includes improvements to read trimming. The tool can produce high-quality microbial genome assemblies on a laptop computer and recovers a more complete set of reference genes than previous methods.