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Old 05-01-2013, 01:37 PM   #1
Location: Newcastle upon Tyne

Join Date: Apr 2013
Posts: 55
Default Iontorrent denovo and reference assembler tools

Hi everyone, I am doing my master's thesis on evaluation of de-novo and reference guided assemblies.

I am using iontorrent fastq and sff files.

I have already got ray and mira in my list.

The other tools like velvet gives extremely short reads. Can you suggest with a series of other tools please that will provide a good assembly. SOApdenovo and ABYss are for shorter reads.

Could someone help me with the reference assemblies as well please?

Thank you.
pari_89 is offline   Reply With Quote
Old 05-02-2013, 01:42 AM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

Try the Roche 454 'Newbler' gsAssember too, I've heard it works well with IonTorrent data too.
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Old 05-14-2013, 05:23 AM   #3
Location: Newcastle upon Tyne

Join Date: Apr 2013
Posts: 55

Thank you, I have tried Newbler and it gives good results. By the way, any suggestions for reference-guided assembly tools??

I need to do a performance evaluation of reference against an assembly for mulitiple tools using Ion torrent data.

Thank you
pari_89 is offline   Reply With Quote
Old 05-14-2013, 07:47 AM   #4
Location: Berlin

Join Date: Oct 2010
Posts: 71

Scripture and Cufflinks should be on your list for reference-guided / mapping assembly.
rboettcher is offline   Reply With Quote

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