NextGenOptimator is a project dedicated to developing software tools for the analysis of output from genome sequencing and assembly pipelines.

Currently we have three main software tools to offer:

a5 pipeline

A genome assembly pipeline for bacteria and archaea that automates as much data cleaning and parameter selection as possible. To get A5, please visit our downloads page.

Then see the README for details on using the pipeline.

Mauve Assembly Metrics

A system to assess the quality of a genome assembly against a finished reference genome under a variety of metrics. See here for usage instructions and over here for examples of output.

miscellaneous tools

These include tools to re-pair paired-end reads after some have been filtered, generate summary statistics on assemblies, and other miscellaneous tasks.