Scientific Informatics Solutions

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Next Generation Sequencing Informatics

IFXworks offers a comprehensive collection of informatics services for Next Generation Sequencing (NGS). In the recent months, we have participated in many genomics and transcriptomics projects in collaboration with leading academic, government and commercial organizations. In particular, we have produced genomes for a number of bioenergy and environmental sentinel species.

This diagram illustrates a typical high-level work flow in a NGS project.

Starting with raw reads provided by the customer, we execute our state-of-art sequence assembly and annotation pipeline. Features include:

Sequence assembly algorithms. We have used various NGS assembly algorithms: TGICL, MIRA, OASES, and reviewed many more, including SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and can recommend specific technology and parameter settings for your problem, that would lead to the most accurate results.

Identify genes, detect mutations and SNPs in the raw sequence. Please have a look at our review of the gene finding methods and benchmarks for gene finding (Full Text) or inquire about our manual data curation capability.

Functional annotation by comparison to leading international sequence (NCBI RefSeq, NR) and protein domain model (InterPro) databases, 3D structure threading, and mapping to pathway and medical information resources. Additional advanced functional analysis is available on request. In particular, we provide Gene Set Analysis (GSEA), Genome-Wide Association (GWAS), haplotype, comparative genomics, and computational biomarker discovery studies. Please contact us to discuss these capabilities.

Software is deployed on our own Linux cluster or on the compute cloud, as problem size demands. We possess extensive experience in conversion of bioinformatics algorithms for cloud computing platforms. We take care of the maintenance and support of our high-performance computing resources, freeing your time to do real science. Also, our high-performance computing expertise means that no problem is too big. In fact, we pride ourselves on being able to execute compute tasks of extremely large capacity. All results are made available in multiple ways to suit your business process. Our presentation servers allow for secure sharing of results with your colleagues. We offer a user-friendly, interactive on-line genome browser. We also make this tool available for in-house licensing, and provide data for download into your database system. Information is available in multiple industry-standard and custom formats, including GFF, XML, Oracle export, and delimited ASCII text.

In addition to custom development, we are now also offering Simbiot, an on-line software for analysis of Next Generation Sequencing and Microarray Expression data sets. Simbiot is developed by the Japan Bioinformatics KK, of which IFXworks LLC is an authorirized distributor. A more detailed description of Simbiot, as well as a link to set up a trial account, is available here.

Our pricing is the most competitive in the industry.
Contact us for a pre-print on our recent genomics efforts.

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