inGAP: an integrated next-generation genome analysis pipeline Export

@article{citeulike:6055558, abstract = {Summary: We develop a novel mining pipeline, Integrative Next-generation Genome Analysis 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. 10.1093/bioinformatics/btp615}, author = {Qi, Ji and Zhao, Fangqing and Buboltz, Anne and Schuster, Stephan C.}, citeulike-article-id = {6055558}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp615}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/btp615v1/.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/btp615v1/.full.pdf}, citeulike-linkout-3 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/1/127}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19880367}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19880367}, day = {1}, doi = {10.1093/bioinformatics/btp615}, issn = {1460-2059}, journal = {Bioinformatics}, keywords = {454, coverage, ingap, pipeline, sequencing, snp, snp-discovery}, month = {January}, number = {1}, pages = {127--129}, posted-at = {2009-11-02 21:10:08}, priority = {5}, title = {inGAP: an integrated next-generation genome analysis pipeline}, url = {http://dx.doi.org/10.1093/bioinformatics/btp615}, volume = {26}, year = {2010} }

TY - JOUR ID - citeulike:6055558 L3 - citeulike-article-id:6055558 N2 - Summary: We develop a novel mining pipeline, Integrative Next-generation Genome Analysis 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. 10.1093/bioinformatics/btp615 IS - 1 JF - Bioinformatics SN - 1460-2059 EP - 129 TI - inGAP: an integrated next-generation genome analysis pipeline VL - 26 SP - 127 KW - 454 KW - coverage KW - ingap KW - pipeline KW - sequencing KW - snp KW - snp-discovery AU - Qi, Ji AU - Zhao, Fangqing AU - Buboltz, Anne AU - Schuster, Stephan PY - 2010/01/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btp615 ER -