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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Soapdenovo 2.04

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This is version 2.04 of the Soapdenovo genome assembler

Quick Start

Test Data

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Test data for this app appears directly in the Discovery Environment in the Data window under CommunityData>iplantcollaborative>example_data>Soapdenovo-1.05.

Input File(s)

Use frag_1.fastq and frag_2.fastq from the directory above as test input.

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.

  • Use these parameters within the DE app interface:
    • maximum read length - 100
    • kmer setting - 39
    • insert size - 180
    • read file format - fastq
    • read orientation - normal (fr)
    • library steps - 3
    • library rank for scaffolding - 1
    • output prefix - SoapOutputFrag

Output File(s)

Expect a series of files starting with the output prefix as output. For the test case, the output files you will find in the example_data directory is named SoapOutputFrag.scafSeq, SoapOutputFrag.contig.

Tool Source for App

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