Iontorrent denovo and reference assembler tools

pari_89 · 05-01-2013, 01:37 PM

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.

maubp · 05-02-2013, 01:42 AM

Try the Roche 454 'Newbler' gsAssember too, I've heard it works well with IonTorrent data too.

pari_89 · 05-14-2013, 05:23 AM

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

rboettcher · 05-14-2013, 07:47 AM

Scripture and Cufflinks should be on your list for reference-guided / mapping assembly.

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05-01-2013, 01:37 PM	#1
pari_89 Member Location: Newcastle upon Tyne Join Date: Apr 2013 Posts: 55	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.

05-02-2013, 01:42 AM	#2
maubp 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.

05-14-2013, 05:23 AM	#3
pari_89 Member 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

05-14-2013, 07:47 AM	#4
rboettcher Member Location: Berlin Join Date: Oct 2010 Posts: 71	Scripture and Cufflinks should be on your list for reference-guided / mapping assembly.