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Old 01-13-2010, 05:48 AM   #1
nickloman
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Default 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
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Old 04-30-2010, 10:12 AM   #2
sowmyai
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Hello Nick

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

Sowmya
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Old 05-04-2010, 12:58 AM   #3
rglover
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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.
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Old 05-04-2010, 12:41 PM   #4
nickloman
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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.
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Old 05-05-2010, 07:21 PM   #5
KevinLam
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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

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