Analysis for Paired end reads

[JimC]

I've searched the forums at least a little bit and I'm not seeing any discussions on analysis of paired end reads. I'm having more and more bioinformatics requests for genome resequencing experiments with experimental design based on using part or all of the expt to contain paired end reads from larger genomic fragments. 2Kb ,etc These requests are not limited to a platform so I'm going to have to be dealing with paired end data from both Illumina and Roche 454. I'm in the process of creating some simulation scripts for both data coming from either platform to assess indel and mutation detection.

Can anyone point me to a thread I missed (I've read through most all the main thread on software tools) -- or can we begin a discussion on this type of analysis?

thanks

Jim

[Lee Sam]

Hey Jim!

Have you taken a look at Velvet for the assembly of paired end reads? Elliott Margulies gave a talk about using Velvet on BAC-size segments of the genome to build little contigs and then meta-assembling those with the minimus assembler. You're already using Edena, right?