Velvet assembler

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.

The manipulation of de Bruijn graphs as a method for alignment became more realistic but further developments were needed to address issues with errors and repeats.

[3] This led to the development of Velvet by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute in the United Kingdom.

The following figure shows an example of a de Bruijn graph generated with Velvet: The same process is simultaneously done with the reverse complement of all the k-mers to take into account the overlaps between the reads of opposite strands.

Velvet erases these errors after completion of the Tour Bus algorithm, applying a simple coverage cut-off that must be defined by the user.

For more detail and examples refer to the Velvet Manual [5] Current DNA sequencing technologies, including NGS, are limited on the basis that genomes are much larger than any read length.

The connections between the reads become more indistinct due to the decrease in overlapping sections leading to a greater possibility of errors.

To overcome these issues, dynamic sequencing programs that are efficient, highly cost effective and able to resolve errors and repeats were developed.

Figure 1: Example of read hashing and respective de Bruijn graph
Figure 2: Simplified de Bruijn graph
Figure 3: Example of tips
Figure 4: Example of bubble erase
Figure 5: Example of bubble detection