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Genomic Software Solutions get Spotlight at AGBT

Abizar Lakdawalla, Ph.D.
| Feb 14, 2014

At Tuesday’s opening plenary sessions, NHGRI’s Eric Green announced a meeting pattern change. A new type of session, software demonstrations, would offer an alternative format to static posters or in-suite presentations. This first of its kind session was held Thursday at the nearby Hilton property with approximately 30 vendors giving one-on-one or small group software demos. The Illumina BaseSpace team was there to show BaseSpace Onsite and the RNA Core Apps, and were kept busy by a steady stream of inquiries.

I’m glad that the AGBT organizers added this session, as was the general consensus of many at this well-attended event. Having a mind-bending spread of food and drink (chocolate fountain, sushi, sliders, crab, fried rice; I could go on and on) is a great hook for getting scientists to migrate off property and try something new.

I’ve listed the vendors with their software tools on display (in alphabetical order), let me know if I missed anyone.

Agilent: SureCall - raw sequencing data from HaloPlex and SureSelect panels processed for adaptor sequence removal, aligned, mutations called, functional annotations.
Albert Einstein College of Medicine: Wasp software links LIMS and analytical pipelines, with metadata capture and high-performance computing management (jobs to local, cloud or grid) .
Annai Systems: Data access portal for data repositories with automatic  meta-data indexing, user queries without the need to move files across the Internet.
Ayasdi: Topological Data Analysis to  cancer types, analysis of breast cancer map showing subtypes of cancer patients.
Bina Technologies: Whole Genome, Whole Exome, Targeted Panels, and RNA-Seq, and cancer analysis workflow on cloud or on-premise. Bina data management and analytics engine for large cohort studies.
Biomatters: Geneious R7 to query, manage, analyze, and share sequence data
Biomatters Melanoma Profiler  melanoma.tumor/normal comparative variant analysis, gene expression, patient survival, drug targets, clinical trials.
DNAnexus: PAAS (Platform as a Service) with command-line tool or web-based interface.  
DNASTAR: Software for alignment, SNPs and small indels calling, gene coding impact on a desktop computer or cloud. Gene Ontology (GO) annotations for pathway-level effects.
Enzymatics: Archer NGS assay design tools for detection of SNVs, indels, CNVs and fusion transcripts.  
Food & Environment Research Agency United Kingdom: Bioinformatics methods for identifying nonsynonymous SNPs referenced to protein mass shifts, to detect protein variants, of bacteria involved in food safety and in public health.
GenoLogics: Clarity Run Manager, no-cost solution for light NGS sample and project tracking, pooling and index assignment, and automatic sample sheet generation.
GenomOncology: Analysis of Cancer Genome Atlas DNA, RNA, methyl arrays. Filters for samples, gene, variation; converts raw sequencing data into actionable report.
HudsonAlpha Institute for Biotechnology: Tool supporting tile-level analytics on sequencing runs based on Illumina’s interop run folders correlated with reagent lot numbers and sample identifiers allows robust analytics to be visualized at the project, instrument, sample type, or run type level.  
Illumina: BaseSpace On-premise and cloud platforms that provide data staorage and analysis tools for RNA and variation detection.
Ingenuity: Variant Analysis, expert-curated mutation and biomedical database. Druggable pathway analysis.
Lab7: Workflow management for NGS; sample tracking, protocols management, pipeline manager of analysis software and reporting.  
Life Tech:  Ion Reporter suite for analysis, annotation, archiving, and reporting of sequencing data. Access to dbSNP, COSMIC, OMIM, ClinVar . AmpliSeq™ Designer software, for custom panels.
NRGENE: GenoMagic for plant breeding does de-novo assembly of plant exomes (yes). Uses allele distribution, genetic maps and phenotypic information. QTLs. Examples from Rice, Tomato and Maize.
Oklahoma Med Res Foundation: GenomeRunner - classification of SNVs  in similar traits or diseases based on similar epigenomic features.
Omicia: Opal based on VAAST for prioritizing disease variants from exome and genome sequencing of affected individuals and families.
Penn State: Improvements on the Galaxy platform for genomic analysis by acquiring 10 Gb/s network connections to Extreme Science and Engineering Discovery Environment (XSEDE) and deploying datasets into the Integrated Rule-Oriented Data System (iRODS)
SGI-DNA: Archetype, a web service and software framework for comparative analysis of microbial and eukaryotic genomes, metagenomes, and transcriptomes with automated taxonomic assignment, comparative pathway analysis.
Station X: GenePool GUI software “widgets” for  identification of  1000 Genomes frequency distribution, SNPEff impact, and many other relevant annotations in 100’s – 1000’s of genomes/exomes/transcriptomes.
Strand Life Sciences: Avadis NGS CNV detection based on read-depth to estimate average ploidy, % normal cell contamination off cancer and CNVs.
Washington Univ Sch Medicine: Drug-Gene Interaction database (DGIdb) with 2,611 genes and 6,307 drugs involved in 14,144 drug-gene interactions, and 6,761 genes that belong to one or more of 39 druggable gene categories.