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  • PubMed: inGAP: an integrated next-generation genome analysis pipeline.

    Syndicated from PubMed RSS Feeds

    inGAP: an integrated next-generation genome analysis pipeline.

    Bioinformatics. 2009 Oct 30;

    Authors: Qi J, Zhao F, Buboltz A, Schuster SC

    SUMMARY: We develop a novel mining pipeline, inGAP, guided by a Bayesian principle to detect single nucleotide polymorphisms (SNPs), insertion/deletions (indels) by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. inGAP can be applied to the mapping of both Roche/454 and Illumina reads with no restriction of read length. Experiments on simulated and experimental data show that this pipeline can achieve overall 97% accuracy in SNP detection and 94% in the finding of indels. All the detected SNPs/indels can be further evaluated by a graphical editor in our pipeline. inGAP also provides functions of multiple genomes comparison and assistance of bacterial genome assembly. AVAILABILITY: inGAP is available at http://sites.google.com/site/nextgengenomics/ingap CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

    PMID: 19880367 [PubMed - as supplied by publisher]



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  • #2
    Has anyone tried this out?

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    • #3
      Originally posted by johnwhitaker View Post
      Has anyone tried this out?
      I just installed it, but can't get the demo(s) to work. I can start it up like explained on this site http://sites.google.com/site/nextgengenomics/ingap , and click the demo button, but when I try to start Demo 1 it gives a bunch of errors:

      it says it can't find the file:
      <..cut..>/inGAP_linux64/demo/demo1/PROJECT/CONTIG_1\inGAP.log

      <..cut..>
      Reading Genome: NOT_AVAILABLE
      Error[5] file not found: NOT_AVAILABLE
      Exception in readGenomeSequence()
      file format error: NOT_AVAILABLE
      0 bps loaded
      -1 -1 -1 -1 -1
      <..cut..>

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