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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Velveth-1.2.10

Velveth, the first stage, is 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

  • To use Velveth-1.2.10, import your data in fastq, fasta, sam, bam, eland or gerald format. Paired reads must be in interlaced format.
  • 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

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.

read type: short paired

Separate vs Interleaved: interleaved

Leave all other parameters in their default settings.

Output File(s)

Expect 2 files as output:

  1. Roadmaps
  2. Sequences

 

Tool Source for App

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