User: Wbkoets

Name: Wbkoets

Joined: Wednesday 04 November 2009 11:44:43 (UTC)

Last seen: Friday 17 September 2010 15:50:32 (UTC)

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Location: Groningen, Netherlands

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Field/Industry: Bioinformatics

Occupation/Role(s): student

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Hanze University of Applied Sciences, Groningen, the Netherlands
UMC Groningen, the Netherlands - Genetics department

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Taverna 2

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Wbkoets

BowtieToPileup (1)

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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 ...

Created: 2010-09-16

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