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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Professor of Pharmaceutical Sciences at Southern Illinois University. Subject of the Personal Genomes Project with CGI genome sequencing, funded by a university seed grant. Annotated human and mouse genomes at the Washington University (St. Louis) GSC during Bob Waterston's tenure. Worked in nematode gene discovery at Divergence, Inc. Recent NSF grant in yeast recombinant genetics. Teach pharmacogenomics, human genomics and pharmaceutical biotechnology. -
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.Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
Projects: U87MG whole genome sequence [Website] [Paper] -
Are there any published metrics on DNAnexus' aligner performance or is it just word-of-mouth for now?Comment
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Not that I know of, but they just started offering bwa as an alternative mapping approach to their proprietary method.Professor of Pharmaceutical Sciences at Southern Illinois University. Subject of the Personal Genomes Project with CGI genome sequencing, funded by a university seed grant. Annotated human and mouse genomes at the Washington University (St. Louis) GSC during Bob Waterston's tenure. Worked in nematode gene discovery at Divergence, Inc. Recent NSF grant in yeast recombinant genetics. Teach pharmacogenomics, human genomics and pharmaceutical biotechnology.Comment
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That is interesting, and probably a good decision to support the needs of the community.Comment
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