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.

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

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

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