Velvet FAQ

#Frequently Asked Questions

##Velvet

Is there a mailing list for Velvet?

Yes - you can subscribe and you can look at the archives.

Does Velvet handle 'N' bases in my reads?

Velvet only supports the A,G,T,C alphabet. Any other characters are converted to 'A'. If you do not desire this behaviour, please remove these reads before giving them to Velvet.

Why do the sequences in contigs.fa have 'N's in them?

If you have paired end reads, and scaffolding is enabled, sometimes Velvet is able to determine that two contigs are joined, but there is not enough read evidence to determine the intervening sequence completely. In this case it inserts a run of Ns the length of which is its estimated number of unknown bases.

Where can I get test data sets for Velvet?

Two small test sets are included with the Velvet source code distribution in the data subdirectory. If you want real data, the Sequence Read Archive (SRA) stores sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome Analyzer®, Applied Biosystems SOLiD® System, Helicos Heliscope®, and others.

##VelvetOptimiser

Is there a mailing list for VelvetOptimiser?

No - please use the Velvet mailing list.