inGAP: an integrated next-generation genome analysis pipeline.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 19880367.
- Also identified by DOI 10.1093/bioinformatics/btp615 and PMC identifier 2796817.
- Licence recorded as CC BY-NC.
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Abstract
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. inGAP is available at http://sites.google.com/site/nextgengenomics/ingap
Medical subject headings
- Algorithms
- Chromosome Mapping
- DNA Mutational Analysis
- Genome
- Polymorphism, Single Nucleotide
- Sequence Analysis, DNA
- Software