Assembly of viral quasispecies

nickloman · 01-13-2010, 05:48 AM

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 · 04-30-2010, 10:12 AM

Hello Nick

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

Sowmya

rglover · 05-04-2010, 12:58 AM

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 · 05-04-2010, 12:41 PM

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 · 05-05-2010, 07:21 PM

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:...l.pone.0010256

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

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01-13-2010, 05:48 AM	#1
nickloman Senior Member Location: Birmingham, UK Join Date: Jul 2009 Posts: 356	Assembly of viral quasispecies 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

05-04-2010, 12:58 AM	#3
rglover rg Location: uk Join Date: Dec 2008 Posts: 51	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 Last edited by rglover; 05-04-2010 at 01:13 AM.

05-05-2010, 07:21 PM	#5
KevinLam Senior Member Location: SEA Join Date: Nov 2009 Posts: 203	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:...l.pone.0010256 and velvet http://www.ebi.ac.uk/~zerbino/velvet/ __________________ http://kevin-gattaca.blogspot.com/

04-30-2010, 10:12 AM	#2
sowmyai Member Location: America Join Date: Jan 2010 Posts: 27	Hello Nick I am looking for a similar solution. Did you happen to come across anything helpful ? Sowmya

05-04-2010, 12:41 PM	#4
nickloman Senior Member Location: Birmingham, UK Join Date: Jul 2009 Posts: 356	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.