PARSES: A Pipeline for Analysis of RNA-Sequencing Exogenous Sequences, is a pipeline constructed from existing sequence analysis tools that allows the user to interrogate RNA-Sequencing experiments for possible biological contamination or the presence of exogenous sequences that may shed light on other factors influencing an organism's condition. Built upon Rake, PARSES allows data simple analysis of RNA-Sequencing data in an automated and repeatable fashion. Usability, logging, and versatility are the keynotes of this pipeline.
Consider visualizing genome coverage of organism after DeNovo Assembly.