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Old 03-11-2011, 12:31 PM   #1
k-gun12
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Default Assembling very large reads

Newbler and Celera have maximum read lengths of ~2048bp I believe. I've got a few libraries of Sanger random shear that have read lengths a little larger than that. I've also got several libs of 454 data, assembled with newbler into contigs, and several libs of Illumina, assembled with velvet and/or CLC into contigs. What's the best option to overlap all these (reasonably large) contigs into a new assembly?
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Old 03-11-2011, 04:10 PM   #2
nickloman
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I always reach for some "standard" overlap assembler like phrap or AMOS-minimus. Although it doesn't always work as well as I'd like / expect. Interested to hear your experiences. Celera might be another option.
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Old 03-12-2011, 08:06 AM   #3
ericgdp
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Cap3 can be one possibility too. Velvet also work to long reads with "-long" parameter.
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