Velvet questions

[dicty]

I just installed Velvet for assembling, but have some questions to ask.

1. Should I use data after alignment or not? Why fastq file without alignment is accepted by velveth?

2. How to run sequence assembling against a reference genome with Velvet? The Velvet manual is too simple and confusing.

Thanks a lot,

Dicty

[Thorondor]

after what alignment???

velveth does not use quality values of fastq files but velvet just does not care if you give the reads in fastq or fasta format.

velvet does not support an assembly with a reference genome! for that you need the extension columbus: http://www.ebi.ac.uk/~zerbino/velvet/

how can the velvet be too simple and also too confusing. Just give it a try you will see it's quite easy. ;-)

[dicty]

I thought Velvet is for assembling with a reference genome. This is why I was confused.