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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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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]
More...
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