General Information
| Description | An integrated next-generation genome analysis pipeline |
| Homepage | http://sites.google.com/site/nextgengenomics/ingap |
Publications
inGAP: an integrated next-generation genome analysis pipeline
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.
Related Tools
PyroHMMvar
Published August 2013
A sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data
MATE-CLEVER
Published September 2013
Mendelian-inheritance-aware discovery and genotyping of midsize and long indels
ISRNA
Published December 2013
An integrative online toolkit for short reads from high-throughput sequencing data
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