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-small-1.0.4

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This is the Soapdenovo-Trans transcript assembler from BGI. This version runs on the Lonestar server at the Texas Advanced Computing Center and has 64 GB of ram available, which is adequate for smaller transcriptomes.

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. Enter them in the boxes for Library 1. 

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.

In parameters enter 78 for the longest read length. For Library 1: 3 for assembly steps, 1 for scaffolding order. Enter 29 for the kmer setting. The rest of the settings can be left as they are.

Output Files

Expect many useful files prefixed with SoapTransOut as output. In the example data section, SoapTransOut.scafSeq and SoapTransOut.scafStatisitics from the test assembly are given.

Tool Source for App

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