| CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. | |
| | |
MedLine Citation:
|
PMID: 23051646 Owner: NLM Status: Publisher |
Abstract/OtherAbstract:
|
Whole genome sequencing (WGS) allows researchers to pinpoint genetic differences between individuals and significantly shortcuts the costly and time-consuming part of forward genetic analysis in model organism systems. Currently, the most effort-intensive part of WGS is the bioinformatic analysis of the relatively short reads generated by second generation sequencing platforms. We describe here a novel, easily accessible and cloud-based pipeline, called CloudMap, which greatly simplifies the analysis of mutant genome sequences. Available on the Galaxy web platform, CloudMap requires no software installation when run on the cloud, but it can also be run locally or via Amazon's Elastic Compute Cloud (EC2) service. CloudMap uses a series of pre-defined workflows to pinpoint sequence variations in animal genomes, such as those of pre-mutagenized and mutagenized Caenorhabditis elegans strains. In combination with a variant-based mapping procedure, CloudMap allows users to sharply define genetic map intervals graphically and to retrieve very short lists of candidate variants with a few simple clicks. Automated workflows and extensive video user guides are available to detail the individual analysis steps performed (http://usegalaxy.org/cloudmap). We demonstrate the utility of CloudMap for WGS analysis of C. elegans and Arabidopsis genomes and describe how other organisms (e.g. Zebrafish, Drosophila) can easily be accommodated by this software platform. To accommodate rapid analysis of many mutants from large scale genetic screens, CloudMap contains an in silico complementation testing tool which allows users to rapidly identify instances where multiple alleles of the same gene are present in the mutant collection. Lastly, we describe the application of a novel mapping/WGS method ("Variant Discovery Mapping") that does not rely on a defined polymorphic mapping strain and we integrate the application of this method into CloudMap. CloudMap tools and documentation are continually updated at http://usegalaxy.org/cloudmap. |
| | |
Authors:
|
Gregory Minevich; Danny S Park; Daniel Blankenberg; Richard J Poole; Oliver Hobert |
Related Documents
:
|
1624436 - Cloning of a methanol-inducible moxf promoter and its analysis in moxb mutants of methy... 12007666 - Transcriptional analysis of the reca gene in streptomyces rimosus: identification of th... 10582986 - Functional polymorphism in the matrix metalloproteinase-9 promoter as a potential risk ... 18952156 - Cloning and functional characterization of the ovine malic enzyme promoter. 8875236 - Role of telomeric sequences in murine radiation-induced myeloid leukaemia. 2510296 - Mapping the drosophila genome with yeast artificial chromosomes. |
Publication Detail:
|
Type: JOURNAL ARTICLE Date: 2012-10-11 |
Journal Detail:
|
Title: Genetics Volume: - ISSN: 1943-2631 ISO Abbreviation: Genetics Publication Date: 2012 Oct |
Date Detail:
|
Created Date: 2012-10-12 Completed Date: - Revised Date: - |
Medline Journal Info:
|
Nlm Unique ID: 0374636 Medline TA: Genetics Country: - |
Other Details:
|
Languages: ENG Pagination: - Citation Subset: - |
Affiliation:
|
Columbia University Medical Center; |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
|
|
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: A Comprehensive Genetic Approach for Improving Prediction of Skin Cancer Risk in Humans.
Next Document: The Transmembrane Proteins UNC-40/DCC, PTP-3/LAR, and MIG-21 Control Anterior-posterior Neuroblast M...