General information
1.2.03 version. Velvet is a set of algorithms manipulating de Bruijn graphs for genomic and de novo transcriptomic Sequence assembly. It was designed for short read sequencing technologies, such as Solexa or 454 Sequencing and was developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute. The tool takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.
See also the installed [intlink id=”6200″ type=”post”]ABySS[/intlink] and comparing both we have published article.
How to use
To run velveth or velvetg add in your scripts for the Torque queue system the corresponding command:
/software/bin/velvet/velveth [velvet options]
/software/bin/velvet/velvetg [velvet option]
Performance
Velvet has been compiled with parallel support througth OpenMP. We have measured the perfomance and the results are available in the report about the Velvet performance in the machines of the Computing Service of the UPV/EHU. Velvet uses huge amount of RAM for large calculations and we have measured it. In the report some simple formulas are obtained to predict the use of RAM for their input files, so the researches can know the needed RAM before start the calculations and in this way can plan their research.
See also the installed [intlink id=”6200″ type=”post”]ABySS[/intlink] and comparing both we have published article.
More information
Velvet web page.
Velvet performance in the machines of the Computing Service of the UPV/EHU report.
Velvet and ABySS performance in the machines of the Computing Service of the UPV/EHU, post in the hpc blog.