inGAP: an integrated next-generation genome analysis pipeline
| Item Type |
Journal Article |
| Author |
Ji Qi |
| Author |
Fangqing Zhao |
| Author |
Anne Buboltz |
| Author |
Stephan C Schuster |
| URL |
http://www.ncbi.nlm.nih.gov/pubmed/19880367
|
| Volume |
26 |
| Issue |
1 |
| Pages |
127-129 |
| Publication |
Bioinformatics (Oxford, England) |
| ISSN |
1367-4811 |
| Date |
Jan 1, 2010 |
| Extra |
| Journal Abbr |
Bioinformatics |
| DOI |
10.1093/bioinformatics/btp615 |
| Accessed |
2009-12-30 14:23:52 |
| Library Catalog |
NCBI PubMed |
| 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 |
| Title |
inGAP: an integrated next-generation genome analysis pipeline |
| Short Title |
inGAP |
| Date Added |
2009-12-30 09:23 |
| Date Modified |
2009-12-30 09:23 |