A simple example using Velvet

How-to: Assembly
A simple example using Velvet
Velvet
“Velvet is an algorithm package that has been
designed to deal with de novo genome assembly and
short read sequencing alignments. This is achieved
through the manipulation of de Bruijn graphs for
genomic sequence assembly via the removal of
errors and the simplification of repeated
regions.”(Zerbino and Birney, 2008)
How does Velvet work?
K-mers: an example with
4mers
K-mers: an example with
4mers
Error handling by velvet
How to run velvet:
•
Two modules:
•
velveth - hash/k-mer construction
•
velvetg - genome assembly
velveth
•
Velveth helps you construct the dataset for the
following program, velvetg, and indicate to the
system what each sequence file represents.
•
Velveth takes in a number of sequence files,
produces a hashtable (k-mer table), then outputs
two files in an output directory (creating it if
necessary), Sequences and Roadmaps, which are
necessary to velvetg.
velveth
velvetg
•
Velvetg is the core of Velvet where the de Bruijn
graph is built then manipulated.
velvetg
Summary
velveth
velvetg