Univa Grid Engine in Life Science

Grid Engine has become the standard in many bioinformatics, chemistry and genomics computing environments. Life science users have increasingly turned to Univa for enterprise-grade support and innovation for their mission-critical computing requirements necessary to drive biomedical research and drug development processes.

Read about applications that are integrated with Grid Engine:

illumina Illumina CASAVA
www.illumina.com

Consensus Assessment of Sequence And VAriation (CASAVA) is the part of Illumina's sequencing analysis software that performs alignment of a sequencing run to a reference genome and subsequent variant analysis and read counting.

PacBio PacBio SMRT Analysis
www.pacificbiosciences.com

Pacific Biosciences delivers SMRT Analysis software, a suite of secondary analysis tools capable of processing sequencing data in real-time. Due to the nature of single molecule, real-time (SMRT) sequencing, it is imperative that the secondary analysis keeps pace with the speed of the instrument. The application is integrated with Grid Engine via DRMAA.

lifetechnologies Ion Torrent
ioncommunity.lifetechnologies.com

Ion Torrent uses semiconductor technology to deliver the fastest benchtop next-gen sequencing. Ion semiconductor sequencing is a method of DNA sequencing based on the detection of hydrogen ions that are released during the polymerization of DNA.

broadinstitute GATK
www.broadinstitute.org

The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. GATK offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine, Grid Engine job submitter and high-performance computing features make it capable of taking on projects of any size.

schrodinger Schrödinger
www.schrodinger.com

Schrödinger is a scientific leader in computational chemistry, providing software solutions and services for life sciences and materials research. Schrödinger has a huge commercial ISV package which is used by researchers doing drug design, chemistry or molecular modeling work. The ISV package is fully integrated with Grid Engine.

CLC Bio CLC Bio NGS Analysis Software
www.clcbio.com

CLC Genomics Workbench, for analyzing and visualizing next-generation sequencing data, incorporates cutting-edge technology and algorithms, while supporting and integrating the rest of a typical NGS workflow.

galaxyproject Galaxy NGS Workflow Software
galaxyproject.org

Galaxy is an open, web-based platform for data intensive biomedical research. Whether on a free public or private server, one can perform, reproduce, and share complete analyses. The Galaxy Team is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.

slipstream Slipstream
bioteam.net/slipstream

Galaxy Edition offers a powerful dedicated resource for data analysis and reduces the IT and administrative burden of running a production instance of Galaxy. It offers a powerful dedicated resource and, like the Galaxy platform, is designed to lower the barrier to entry into data analysis. NGS Edition is a customized appliance specifically designed to support the needs of managing and analyzing NGS data. The solution provides a centralized system to integrate sequencing instruments, store and manage NGS data, and run downstream analyses.

hubzero HUBzero Scientific Application Portal
hubzero.org

HUBzero is an open source software platform for building powerful Web sites that support scientific discovery, learning, and collaboration. Originally created by researchers at Purdue University in conjunction with the NSF-sponsored Network for Computational Nanotechnology to support nanoHUB.org, the HUBzero platform now supports dozens of hubs across a variety of disciplines, including cancer research, pharmaceuticals, biofuels, climate modeling, microelectromechanical systems, water quality, volcanology, and more.

biobwa BWA
bio-bwa.sourceforge.net

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment and are designed for longer sequences ranged from 70bp to 1Mbp.

BLAST BLAST+
blast.ncbi.nlm.nih.gov

BLAST (Basic Local Alignment Search Tool) is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. BLAST finds regions of local similarity between sequences.

EMBOSS EMBOSS
emboss.sourceforge.net

EMBOSS (The European Molecular Biology Open Software Suite) is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, extensive libraries are provided with the package allowing other scientists to develop and release software in true open source spirit.

ncbi NCBI_Toolkit
www.ncbi.nlm.nih.gov/toolkit

The NCBI C++ Toolkit is a public-domain collection of portable libraries consisting of a cross-platform application framework and a set of utilities and supporting classes to work with biological data.

KNIME KNIME
www.knime.org

KNIME is the leading open platform for data-driven innovation helping organizations to stay ahead of change. Innovative organizations use KNINE open-source, enterprise-grade analytics platform to discover the potential hidden in their data, mine for fresh insights, or predict new futures.

abyss ABySS
www.bcgsc.ca

ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.