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.
- 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 for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Velvet > velveth
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.
Expect 2 files as output: