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-Trans 1.0

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This is the Soapdenovo-Trans transcript assembler from BGI.

Quick Start

Test Data

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

Input File(s)

Use BA_1.norm.fq and BA_2.norm.fq 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 78 for the maximum read size.
    • 27 for kmer setting.
    • 400 for paired-end spacing.
    • SoapOutput for the output prefix.
    • Normal Orientation.
    • Library steps 3.
    • Scaffolding rank 1.
    • Input sequence format fastq.
    • Run time 4 hrs., bigger assembly.
    • Leave other settings at default.

Output File(s)

Expect a large number of files as output. For the test case, the important output files you will find in the example_data directory are SoapOutput.scafSeq, and SoapOutput.scafStatistics. The scafStatistics file has a series of statistics for the assembly in scafSeq.

Tool Source for App

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