BowtieToPileup

This example workflow aligns short sequencing reads to a reference genome using Bowtie and generates a SAMtools pileup file. By analysing an actual data set (SNP detection in N. vitripennis) and translating this analysis pipeline into a Taverna workflow, I was able to come up with an easy way of using Taverna for such analysis. I created a Java API (with my limited Java experience) that wraps the command line programs used in the analysis pipeline: Bowtie and some of the SAMtools. Instead of passing Taverna or the API data, only references to files are used. The API does not have a main entry point, instead, each step in the analysis pipeline is represented by a short Beanshell script that calls the appropriate method of the API. These scripts are used as services. This workflow is part of my bachelors thesis (bioinformatics at the Hanze University Groningen, the Netherlands). Please note that Bowtie and the SAMtools need to be installed and in the path. The API needs to be present in the .taverna/lib directory, please check dependencies of the Beanshell services. Assumes Linux.