Document Detail


CloudMap: a cloud-based pipeline for analysis of mutant genome sequences.
MedLine Citation:
PMID:  23051646     Owner:  NLM     Status:  MEDLINE    
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 predefined workflows to pinpoint sequence variations in animal genomes, such as those of premutagenized 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 and 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 that 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 :
24046776 - Meta4: a web application for sharing and annotating metagenomic gene predictions using ...
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 ...
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; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2012-10-10
Journal Detail:
Title:  Genetics     Volume:  192     ISSN:  1943-2631     ISO Abbreviation:  Genetics     Publication Date:  2012 Dec 
Date Detail:
Created Date:  2012-12-05     Completed Date:  2013-06-03     Revised Date:  2013-12-04    
Medline Journal Info:
Nlm Unique ID:  0374636     Medline TA:  Genetics     Country:  United States    
Other Details:
Languages:  eng     Pagination:  1249-69     Citation Subset:  IM    
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:
Animals
Arabidopsis / genetics
Caenorhabditis elegans / genetics
Chromosome Mapping / methods*
Computational Biology / methods*
Computer Simulation
Drosophila / genetics
Genetic Variation
Genome
Internet*
Mutation*
Polymorphism, Single Nucleotide
Reproducibility of Results
Software*
Zebrafish / genetics
Grant Support
ID/Acronym/Agency:
F31 NS074841/NS/NINDS NIH HHS; HG004909/HG/NHGRI NIH HHS; HG005133/HG/NHGRI NIH HHS; HG006620/HG/NHGRI NIH HHS; R01NS039996-05/NS/NINDS NIH HHS; R01NS050266-03/NS/NINDS NIH HHS; //Howard Hughes Medical Institute
Comments/Corrections

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:  Transmembrane proteins UNC-40/DCC, PTP-3/LAR, and MIG-21 control anterior-posterior neuroblast migra...