The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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Mapping illumina seq data Part 1

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Utilizes BWA for mapping of illumina sequencing data. Default settings (customizable) for a species to be mapped to a divergent genome reference and to output a BAM file. Used with; SNP calling illumina seq data Part2 to output SNP calls.

Quick Start

Test Data

Input File(s)

Use one of the files above as test input. Our pseudo wheat genome reference sequence to complement the test datasets (as detailed Gardiner et al., 2014:  doi: 10.1111/tpj.12660) can be found at: http://de.iplantcollaborative.org/dl/d/12BD9EC9-EABF-4B9C-9B31-7143F6FCB126/Wheat_new_array_AH_sequence.fas

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

  • Default parameters only, no further configuration needed.
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Output File(s)

Expect a sorted BAM file as output. For the first test case, the output file you will find at the link: http://de.iplantcollaborative.org/dl/d/58DA9AAF-597F-4BE3-B9F4-ECFA19B583F4/bwa_output.sorted.21668.bam

Tool Source for App

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