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rdf:type |
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lifeskim:mentions |
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pubmed:issue |
1
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pubmed:dateCreated |
2009-12-23
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pubmed:abstractText |
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
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pubmed:commentsCorrections |
http://linkedlifedata.com/resource/pubmed/commentcorrection/19880367-11932250,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19880367-15034147,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19880367-18212088,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19880367-18227114,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19880367-18262675,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19880367-18576944,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19880367-18660809,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19880367-18714091,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19880367-19430453,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19880367-19451168,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19880367-19508981,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19880367-19832984,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19880367-2231712
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:status |
MEDLINE
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pubmed:month |
Jan
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pubmed:issn |
1367-4811
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pubmed:author |
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pubmed:issnType |
Electronic
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pubmed:day |
1
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pubmed:volume |
26
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
127-9
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pubmed:dateRevised |
2010-9-28
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pubmed:meshHeading |
pubmed-meshheading:19880367-Algorithms,
pubmed-meshheading:19880367-Base Sequence,
pubmed-meshheading:19880367-Chromosome Mapping,
pubmed-meshheading:19880367-DNA Mutational Analysis,
pubmed-meshheading:19880367-Genome,
pubmed-meshheading:19880367-Molecular Sequence Data,
pubmed-meshheading:19880367-Polymorphism, Single Nucleotide,
pubmed-meshheading:19880367-Sequence Analysis, DNA,
pubmed-meshheading:19880367-Software,
pubmed-meshheading:19880367-Systems Integration,
pubmed-meshheading:19880367-User-Computer Interface
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pubmed:year |
2010
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pubmed:articleTitle |
inGAP: an integrated next-generation genome analysis pipeline.
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pubmed:affiliation |
Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania 16802, USA.
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pubmed:publicationType |
Journal Article,
Research Support, Non-U.S. Gov't
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