Thanks P.R.Krishna Behra for taking interest . I am learning this plateform so I don't have any samples. I have used Newbler for 454 data so a question come mind that how we do assembly for miseq data. I want know that there is any tool which provieded by illumina company.Finally for 150 bp and 250 bp different protocol use?
I can highly recommend to use SPAdes. It's a new DBG assembler which introduce a nice new approaches to deal with the k-mer-choice problem usually part of DBG assemblers. It also "scores" very high is the already named GAGE-B comparison (so to speak):
http://bioinf.spbau.ru/spades
If you're already familiar with Newbler, you could also give it a try and assemble the MiSeq data with Newbler, you would be surprised how good the results can be.
To answer your question: The assembler used within the Illummina operating software and also the assembler most often used for Illumina data is velvet. However, MiSeq data is longer and velvet may not be the best default choice anymore.
Thanks Sebastain and P.R.Krishna Behra for helping me out. I have gone through GAGE-B article and came to know that there are other assemblers also available not just velvet and Newbler. I haven't used SPAdes yet but I would like to use in future. However , I know its silly question but I want to know that is it appropriate to use illuminas data in 454's tool? I mean I know assembler just do assembly but there must be some reason that why cant we use illuminas data in newbler.
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