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Old 07-21-2011, 07:48 AM   #1
rworthi
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Default assembling Nimblegen exome reads

I just got Nimblegen v2 exome data. I would like to assemble the reads, exon by exon. Is there a program that will do this? DNAnexus maps the reads to the Golden Path and provides variant calls, but they do not provide an assembled sequence for each covered exon.
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Old 07-21-2011, 11:42 AM   #2
Michael.James.Clark
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Why do you want to assemble rather than align the data?

I do not suggest using DNAnexus for mapping/variant calling. Results are quite different from the very accurate results of BWA (or Novoalign) and GATK/Dindel in my experience.
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Old 11-09-2011, 11:15 AM   #3
zee
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Are there any published metrics on DNAnexus' aligner performance or is it just word-of-mouth for now?
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Old 11-09-2011, 11:20 AM   #4
rworthi
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Not that I know of, but they just started offering bwa as an alternative mapping approach to their proprietary method.
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Old 11-09-2011, 11:23 AM   #5
zee
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That is interesting, and probably a good decision to support the needs of the community.
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