SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   Iontorrent denovo and reference assembler tools (http://seqanswers.com/forums/showthread.php?t=29829)

pari_89 05-01-2013 01:37 PM

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.

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.


All times are GMT -8. The time now is 04:27 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.