@article {2,
	title = {Multicore and Cloud-Based Solutions for Genomic Variant Analysis},
	journal = {Euro-Par 2012: Parallel Processing Workshops},
	volume = {7640},
	year = {2013},
	month = {2013},
	chapter = {273},
	abstract = {Genomic variant analysis is a complex process that allows to find and study genome mutations. For this purpose, analysis and tests from both biological and statistical points of view must be conducted. Biological data for this kind of analysis are typically stored according to the Variant Call Format (VCF), in gigabytes-sized files that cannot be efficiently processed using conventional software. In this paper, we introduce part of the High Performance Genomics (HPG) project, whose goal is to develop a collection of efficient and open-source software applications for the genomics area. The paper is mainly focused on HPG Variant, a suite that allows to get the effect of mutations and to conduct genomic-wide and family-based analysis, using a multi-tier architecture based on CellBase Database and a RESTful web service API. Two user clients are also provided: an HTML5 web client and a command-line interface, both using a back-end parallelized using OpenMP. Along with HPG Variant, a library for VCF files handling and a collection of utilities for VCF files preprocessing have been developed. Positive performance results are shown in comparison with other applications such as PLINK, GenABEL, SNPTEST or VCFtools.},
	keywords = {genomic variant analysis, Multicore, Mutation, OpenMP, web service},
	isbn = {978-3-642-36948-3},
	issn = {0302-9743},
	doi = {10.1007/978-3-642-36949-0_30},
	url = {http://rd.springer.com/chapter/10.1007/978-3-642-36949-0_30},
	author = {Cristina Y. Gonz{\'a}lez and Bleda, Marta and Salavert, Francisco and Rub{\'e}n Sanchez and Dopazo, Joaqu{\'\i}n and Medina, Ignacio}
}
@article {5,
	title = {VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing.},
	journal = {Nucleic Acids Res},
	volume = {40},
	year = {2012},
	month = {2012 Jul},
	pages = {W54-8},
	abstract = {The massive use of Next-Generation Sequencing (NGS) technologies is uncovering an unexpected amount of variability. The functional characterization of such variability, particularly in the most common form of variation found, the Single Nucleotide Variants (SNVs), has become a priority that needs to be addressed in a systematic way. VARIANT (VARIant ANalyis Tool) reports information on the variants found that include consequence type and annotations taken from different databases and repositories (SNPs and variants from dbSNP and 1000 genomes, and disease-related variants from the Genome-Wide Association Study (GWAS) catalog, Online Mendelian Inheritance in Man (OMIM), Catalog of Somatic Mutations in Cancer (COSMIC) mutations, etc). VARIANT also produces a rich variety of annotations that include information on the regulatory (transcription factor or miRNA-binding sites, etc.) or structural roles, or on the selective pressures on the sites affected by the variation. This information allows extending the conventional reports beyond the coding regions and expands the knowledge on the contribution of non-coding or synonymous variants to the phenotype studied. Contrarily to other tools, VARIANT uses a remote database and operates through efficient RESTful Web Services that optimize search and transaction operations. In this way, local problems of installation, update or disk size limitations are overcome without the need of sacrifice speed (thousands of variants are processed per minute). VARIANT is available at: http://variant.bioinfo.cipf.es.},
	keywords = {Databases, Genetic Variation, High-Throughput Nucleotide Sequencing, Internet, Molecular Sequence Annotation, Mutation, Nucleic Acid, Polymorphism, Single Nucleotide, Software, User-Computer Interface},
	issn = {1362-4962},
	doi = {10.1093/nar/gks572},
	url = {http://nar.oxfordjournals.org/content/40/W1/W54},
	author = {Medina, Ignacio and de Maria, Alejandro and Bleda, Marta and Salavert, Francisco and Alonso, Roberto and Gonzalez, Cristina Y and Dopazo, Joaqu{\'\i}n}
}
