Posted by: shrikantmantri | November 5, 2009

inGAP: an integrated next-generation genome analysis pipeline.

via Bioinformatics on 11/3/09


Publication Date: 2009 Oct 30 PMID: 19880367
Authors: Qi, J. – Zhao, F. – Buboltz, A. – Schuster, S. C.
Journal: Bioinformatics

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: scs@bx.psu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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Posted via email from Sharing significant bytes —(Shrikant Mantri)

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