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 creating a Galaxy version of the pipeline. The Central Galaxy server does not have a de novo assembler so an abbreviated version would have to be created on it, but tools are easy to add to own version. Could fully implement on a local Galaxy server without much effort which would get many benefits such as more data types supported, automatic scheduling, simplified logic, GUI, etc.
Lythimus
commented
13 years ago
Consider creating a Galaxy version of the pipeline. The Central Galaxy server does not have a de novo assembler so an abbreviated version would have to be created on it, but tools are easy to add to own version. Could fully implement on a local Galaxy server without much effort which would get many benefits such as more data types supported, automatic scheduling, simplified logic, GUI, etc.