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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This App runs BWA mem (version 0.7.15) to 

  • Map long read sequencing data (such as Nanopore or PacBio) to a reference genome.

App Creator

Amanda Cooksey

Quick Start

Sequencing files in FASTQ format. For paired-end data there should be two separate files (forward and reverse). For single-end data only the first file is required. 

Reference genome sequence in FASTA format. You can either use a reference provided by CyVerse or provide your own file. 

There are many optional parameters. However, default values are provided. 


Test Data


Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> bwa_mem > longreads

Input File(s)

Use 'SRR6364637_nano.fastq' as the left read file.

Use 'GCF_000686545.1_ASM68654v1_genomic.fna.gz' as the reference genome FASTA file

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 section below.

Check 'Nanopore data' under inputs.

Output File(s)

This app, run with the parameters above, will generate 1 output file: bwa_output.sam.

The analysis folder will also contain the BWA index files made during your analysis. 

Tool Source for App

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