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Velveth, the first stage, the hashing stage of the whole genome assembler. It can also be used with Oases for transcriptome assembly and with Columbus for template-dependent assembly.

Quick Start

Test Data

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

Input File(s)

Use  Interlaced.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 to get the output provided in the next section below.

kmer setting: An odd integer. Typically about 1/2 the read length.

Leave all other parameters in their default settings.

Output File(s)

Expect a VelvetOut.tar.gz as output. 

Tool Source for App