Velveth-1.2.07
- de-confluence
- amcooksey (Unlicensed)
- Branden Lau (Unlicensed)
- Roger Barthelson
Velveth-1.2.07
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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
- To use Velveth-1.2.07, import your data in fastq, fasta, sam or bam format. Paired reads must be in interlaced format.
- Resources: https://www.ebi.ac.uk/~zerbino/velvet/
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.