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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BWA-0.7.4 non-model species

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Index and map short reads to a reference sequence with BWA

App Name

BWA Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. This instance of BWA works with paired-end sequencing reads.

Quick Start

Test Data

Input File(s)

Use 10K_SRR192294_1.fastq (2.4M) http://mirrors.iplantcollaborative.org/example_data/bwa/10K_SRR192294_1.fastq and 10K_SRR192294_2.fastq (2.4M)http://mirrors.iplantcollaborative.org/example_data/bwa/10K_SRR192294_2.fastq as test data. Import from URL to get the data into your Discovery Environment account.

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.

  • Select a reference genome from the list - Brachypodium distachyon (line Bd21) v1
  • All other parameters remain in their default state

Output File(s)

Expect a SAM file named after the input files as output. For the test case, the output file is 10K_SRR192294_1.fastq-10K_SRR192294_2.fastq.sam (4.8M)http://mirrors.iplantcollaborative.org/example_data/bwa/10K_SRR192294_1.fastq-10K_SRR192294_2.fastq.sam

Tool Source for App

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