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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.
- 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/
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.
Expect a VelvetOut.tar.gz as output.