External applications integration: Bowtie

Bowtie [Langmead et al., 2009] is a short-reads mapper that can map sequencing reads to a reference sequence. In this example, we show how to integrate Bowtie via the External Applications functionality.

Here, when they user runs a Bowtie Mapping, they will select their sequencing reads, identify the pre-built index file of the reference sequence to use and set a few parameters via a standard Workbench wizard interface. When the mapping is launched, Bowtie is executed on the system.

To import a SAM or BAM file into the Genomics Server requires both that file and also a copy of the reference genome already in the CLC system. Bowtie itself uses pre-built index files rather than the reference sequences when the mapping is being carried out. However, as the reference sequences for a mapping are required when importing a SAM file, the Post-processing functionality of the External Applications setup allows the administrator to specify how the SAM file should be handled and requires that the user specifies the reference sequences when they set up the job.


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