Version

• Velvet 1.2.03 is available in Hippu

Description

Velvet is a sequence assembler for very short reads

Usage

Velvet does nor require any set up commands. You can use the commands velvetg, velvetg_ds, velveth and velveth_ds to use velvet in Hippu.

Velveth (and the corresponding colorspace version velveth_de) helps you construct the dataset for the following program, velvetg, and indicate to the system what each sequence file represent  Velveth takes in a number of sequence files, produces a hashtable, then outputs two files in an output directory, Sequences and Roadmaps, which are necessary to velvetg. The syntax is as follows:

velveth output_directory hash_length  [[-file_format][-read_type] filename]

For example

velveth assembly_dir 21 -shortPaired data/reads.fa

Velvetg (and the corresponding colorspace version velvetg_de) is the core of Velvet where the de Bruijn graph is built then manipulated. The syntax of velvetg is

velvetg output_directory -options paramters

velvetg assebly_dir -cov_cutoff 5 -read_trkg yes -amos_file yes

By default the maximum k-mer length that can be used  in the hash table is 31 bases. If you wish to use longer k-mers you should use velvet versions that are compiled with lather k-mer size. See the table bellow:

Table 1.  Velvet programs available in Hippu

More information

• Velvet manual
• More information about Velvet can be found form the Velvet home page.