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Old 05-04-2011, 05:29 PM   #1
ndeshpan
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Location: Sydney

Join Date: Nov 2009
Posts: 29
Smile Mira assembler: Medium sized genomes;How to use 2 separate files for paired-end reads

Hi all,

This is Nandan Deshpande from UNSW, Sydney, Australia.

I am working trying to assemble a eukaryotic genome of estimated size of around 400 MB.
I have used SOAPdenovo and produced a rough assembly. As a comparison I am trying to use MIRA assembler. I have few questions:


I have 3 paired-end read data-sets from Illumina Solexa (102 bp ;30917380 reads per file)
With a RAM memory of around 200+ GB can anyone suggest if MIRA has the capacity to assemble these reads? Does it use multiple processors?


Also ..
I am finding difficult to exactly understand the command for MIRA; the nomenclature for the files etc..Is it essential that I have the paired-end reads for a pair in a single file? I have them in two separate files at this time (containing 0/1 and 0/2 reads respectively)..Can anyone who has worked with mira and paired-end reads please paste a sample command with my above requirements?

Does mira help in scaffolding using only paired end reads (insert sizes avg 300bp); but no mate-pairs?

Appreciate all responses..

cheers,

Nandan
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