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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Velvetg-1.2.10

This is the second stage of the Velvet assembler. This app is best suited to smaller datasets as it is not mutlithreaded and requires quite a bit of memory.

Quick Start

  • To use Velvetg-1.2.010, import the tar.gz output directory produced by Velveth -- specifically VelvetOut.tar.gz
  • For large analyses use the Velvet apps marked 'agave' in the system column of the 'apps' window. Apps marked 'de' should only be used for small/bacterial analyses.
  • *Resources: Velvet Manual

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 -> Velvet > velveth > output.

Input File(s)

Use VelvetOut.tar.gz 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.

For the test data, set Read Tracking option to yes (it is transcriptome data). 

Set the Insert Length for small paired reads to 300, and the Insert Length Standard Deviation to 60.

Leave all other parameters in the default setting.

Output File(s)

Expect contigs.fa and VelvetG_Out.tar.gz as output.

Tool Source for App

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