Assembly of viral quasispecies

[nickloman]

Hi all,

Has anyone found software or software settings that work well for assembly of viral quasispecies from 454 reads? Newbler on default settings doesn't work at all well, breaking up into large numbers of very short contigs.

There is an interesting package called "Q Assembler" but this doesn't seem to have been released (http://www.bioinformatics.org/qassembler/wiki/).

Any help appreciated

Nick

[sowmyai]

Hello Nick

I am looking for a similar solution. Did you happen to come across anything helpful ?

Sowmya

[rglover]

Hiya,
I use CLCbio's denovo assembler with the following settings for plant viruses: MM=2,I=3,D-3, Length fraction =0.5, Similariity 0.9. Seems to work pretty well (so far!) especially as we're sequencing direct from the host to get the viral genomes.
Hope that helps,
Rach

[nickloman]

That's good to know. I didn't find anything that particularly helped, although I did briefly consider using PyroNoise on some PCR amplicons from a viral source.

[KevinLam]

have you looked at this?
Characterization of Quasispecies of Pandemic 2009 Influenza A Virus (A/H1N1/2009) by De Novo Sequencing Using a Next-Generation DNA Sequencer

http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0010256

and
velvet
http://www.ebi.ac.uk/~zerbino/velvet/