Custom scripting and special projects

We are a genomics and bioinformatics core facility located within Miami University in Oxford, Ohio, USA. We have an Illumina MiSeq Benchtop Sequencer; an ONT Nanopore minION, an epMotion 5073m NGS Liquid Handling Workstation; an ABI 3130xl Capillary Electrophoresis analyzer (Sanger), a Promega Maxwell16, Agilent Bioanalyzer2100, Sage BluePippin, Covaris M220 ultrasonicator, Qubit 4, Nanodrop (Fluorospectrometer) 3300, BioRad CFX Connect, QuantStudio7, RotorGeneQ (qPCR), several high capacity bioinformatics workstations equipped with both CLC Genomics Workbench and BioBam OmicsBox software, as well as many OS/FOSS software packages.

We are thus able to start from source material and isolate high quality nucleic acid, and construct libraries and perform appropriate QC at each step. We can perform NGS on either the Illumina MiSeq or the ONT minION, as well as comprehensive post-run bioinformatics analyses.

At BioInfoRx, we help scientists obtain biological insights from complex genomic data. We provide complete NGS analytic solutions including standard analysis of raw data, integration between multiple experiments, and online database for data mining and visualizations. We use best-practice open source tools to analyze your raw NGS data, and provide meaningful annotations and downstream data mining tools to help you infer functional insights.

As demonstrated by the numerous publications using our services or web-bases tools, our biology-centric approach has proven effective to decipher molecular mechanisms from genomic data.

Whole Genome Sequencing, Transcriptome Sequencing (RNASEQ /miRNA), Metagenomics, Epigenomics, etc. to our credit; with 100+ co-authorship articles, highest in Indian industry. Recent past, we have also optimized multi-omics Single Cell Genomics solutions to cater to various research needs.

We offer a powerful genomics software platform that makes various bioinformatics tasks fairly straightforward to perform and deliver to customers. We also wrap this product with various service offerings for folks interested in one-off projects that deliver results rather than just subscribing to a software solution and then do the work themselves. We are comfortable with both scenarios. We are well versed in working with RNA-Seq, Genomes, Exomes, targeted panels, miRNA-Seq, Copy Number, Gene Expression, Protein Expression, and DNA Methylation from the level of raw sequencing reads or chip data all the way through to statistically-driven and knowledge-driven interpretations.

Expertise:

We are experienced in developing bioinformatics pipelines, providing data management solutions, analyzing the data using statistical methods and knowledge driven methods, and delivering professional-grade results. We are most familiar with human genomics projects, but have experience with other organisms as well. We are most focused on supporting sequencing projects, but are very capable of supporting array and PCR-based projects as well.

Infrastructure:

We leverage Amazon Web Services for most of our storage (EBS & S3) and computational resources (EC2). We are not frivolous about security, and we can provide you with security documentation to demonstrate how we leverage cloud resources while keeping best-in-class security. We also have powerful 16-core machines in our own private cloud that we leverage for service projects as well.

At NXT-Dx we can offer SE50, PE50 and PE100 sequencing on the Illumina HiSeq. On top of this we can also offer different sequencing settings on the Illumina MiSeq and shortly we will also be able to offer sequencing on the Illumina NextSeq.

We can offer sequencing of already prepared libraries but we can also offer full-scope projects whereby we receive cells, tissue, gDNA or RNA and take care of the sample preparation, library prep, sequencing and bio-informatics analysis.

We have worked with samples from all kind of species (mammalian, plant, bacterial) and all kind of cell types.

We pride ourselves in having close contact with our customers and only one single contact point. Also after the delivery of the data, we remain available to answer any questions customers might have on their data, their analysis, etc.

HybridStat is a company bringing together a team of highly qualified and motivated scientists and developers, whose expertise spans a variety of statistics and computer science domains. Main HybridStat’s services are centered on bioinformatics, biostatistics and analytics of high-throughput data derived from modern biological technologies such as Next Generation Sequencing (NGS), DNA microarrays and Mass Spectrometry. In addition, HybridStat offers customized software solutions regarding the above.

Regarding NGS, HybridStat offers a variety of one-stop shop data analysis and analytics services, spanning from genome alignments and preprocessing of raw short read fragments, up to analytical and specialized reports and figures describing the results of various NGS protocols including RNA-Seq (quality control, differential expression and splicing analysis, biochemical pathway enrichments etc.), ChIP-Seq (data normalization and peak calling, gene-binding site associations, methylation profiles, motif finding etc.), Whole Exome and Whole Genome Sequencing (data preprocessing, variant calling, filtering, annotation and interpretation, etc.) and Single Cell Sequencing data analysis, using both open source and optimized proprietary pipelines.

HybridStat, can also offer complete support to your organization through its advanced Whole Exome Sequencing analytics platform Clingon (www.clingon-mds.com). Clingon is a complete, integrated one-stop clinical genomics and medical decision support platform which performs data analysis from raw data up to the generation of clinical reports. It uniquely integrates and curates a handful of resources regarding gene-disease and gene product-drug associations as well as curated variant annotation data towards more timely and accurate results and the optimal design of personalized treatment plans.

Our facility is unique because we offer the full range of NGS service from sample extraction through to data analysis. Sample extraction capabilities and expertise cover the entire spectrum of both environmental and clinical sample types.

At Diploid, we turn NGS data into clinical reports or research reports, allowing hospitals, commercial labs and research institutes to outsource human genome interpretation.

Our focus is on 3 major areas: - Rare disease diagnostics - Carrier screening - Cancer

With high-quality diagnostics, fast turn-around times, secure infrastructure, and a personal approach, Diploid is rapidly becoming a trusted partner for genetic departments and commercial labs worldwide.

Over the past few months, we have been working for the following institutes and labs: - Oxford University Hospitals (UK) - University of Verona (Italy) - Otogenetics (US) - Macrogen (US) - King Faisal Specialist Hospital (KSA) - National Reference Lab (UAE)

We offer tailored bioinformatics services (mainly NGS data analysis) to academic and private organizations. We have a strong academic background with a focus on cutting edge, open source software.

We build up your in house bioinformatics capacity in 2 ways: First, we provide you with the code underlying the analysis you requested. Second, we can help you to set up (cloud) computing solutions that will allow you to run and extend your analyses independently.

We replicate recommended analysis pipelines (best practice) or develop novel ones but we always emphasize biological interpretation of your data.

Genotypic Technology is the first genomics company based in India with a state-of-the-art, ISO 9001:2008 accredited, SAP-enabled, 12,000 square feet facility in Bangalore. Our high-throughput facility enables us to offer customized services for experiment design consultation, protocol optimization, microarray and probe designing, next-generation sequencing (NGS), and bioinformatics solutions to clients from academia, biotech, and pharma sectors worldwide.

We have been providing high-quality sequencing services, including whole-genome sequencing (WGS), transcriptome sequencing, shotgun metagenome sequencing, and de-novo assembly since 2000. Our skilled team has experience in working with genomes of all sizes and nucleic acids from various sources on Illumina, Oxford Nanopore, and other platforms. We have developed targeted panels for various viruses like Adenovirus, KFDV, SARS-CoV-2, Dengue, and pipelines for predicting virulent strains that may be difficult to treat with conventional antibiotics.

Our broad range of metagenome services includes targeted and whole-genome metagenome and metatranscriptome sequencing. Our long amplicon metagenome approach provides the best resolution of microbes up to the sub-species level, while whole-genome metagenome sequencing enables the identification of gene clusters, resistome, and novel pathways in a given environment. We also specialize in Ribo-footprinting and RNA immunoprecipitation sequencing, ChIP sequencing, and targeted methylation sequencing.

TACGenomics has a team composed of bioinformatician, molecular biologist and computer scientist who are all at Ph.D. level. Our team has the experience of hundreds of NGS data analysis projects from all over the world. The mission of TACGenomics is to help our customer to solve the biological questions. After computation analysis completed by the bioinformatician, our molecular biologist will interpret the analyzed data carefully, provide more insight into your project and help the publication of the project in the high impact journal.

At the forefront of scientific advancement, our sequencing and biorepository facility is part of the One Health Shared Services at Innovation Foundation dedicated to enhancing the health and well-being of humans, animals, and ecosystems.

Our mission: To advance health across boundaries.

Sequencing platforms: NextSeq2000: Versatile Illumina platform for flexibility and speed. MiniSeq: Compact and cost-effective, suitable for targeted sequencing and small-scale applications.

We offer cutting-edge genomic research services & Bioinformatics support. Bioinformatics Support: Our bioinformatics experts collaborate closely with you.

Why Choose Us? Accuracy: Our cutting-edge technology ensures reliable results. Fast Turnaround: Get your data quickly without compromising quality. Expert Support: Our scientists are here to assist you. Custom Solutions: Tailored services to meet your specific research goals. End-to-end solutions: From experimental design to data analysis, we guide you every step of the way.

Contact Us at OHIL@okstate.edu to discuss your sequencing needs or possible collaborations with the One Health Innovation Lab.

The Bioinformatics CRO is a scalable, globally distributed contract research organization and consultancy that provides high quality customized bioinformatics and genomics support to academics, biotechs, and pharmaceutical companies.

genexa is a genomic data analysis provider located in Switzerland. Our bioinformatics services are centered around de novo assembly of genomes and metagenomes. We focus on processing, analysis, and interpretation of your genomics data. For all our fields of expertise, we offer to perform the entire analysis workflow from raw data to documentation, but also consulting and troubleshooting if required. genexa also provides resources to run computationally demanding tasks for specific jobs if you have an existing analysis workflow, but lack the computational resources to run it on large amounts of data. For further information check: genexa.ch

We are TAXON, a data-driven bioinformatics team, specializing in high-confidence downstream analysis and client-ready delivery (not just raw outputs). What makes us unique is that we package sequencing data into actionable, decision-oriented results using reproducible pipelines, ML-ready datasets, and regulatory-grade reporting when needed.

What we specialize

Plasmid-focused analysis: assembly/curation support (incl. circularization checks), plasmid typing/replicons, mobility elements, gene-level annotation, and optional AMR/virulence marker screening when needed.

Microbial genomics & taxonomy: strain identification, ANI/phylogenomics, contamination/QC, comparative genomics, and traceability/fingerprinting.

Metagenomics: end-to-end processing and interpretation for complex communities, including soil metagenomes and waste / residue-derived samples (taxonomic + functional profiling, group comparisons, biomarkers, ML-ready tables).

Yeast & fungal genomics: assembly/QC, annotation, comparative analyses, and applied interpretation for R&D.

Biosynthetic potential (BGC mining): detection, annotation, prioritization, novelty assessment, and clear "what to test next" guidance.

Scientific & regulatory-ready writing: structured, audit-friendly documentation and reports when clients operate in regulated markets.

Custom ML & data science (on request): we develop and productionize ML models for biological/biotech use cases (bioinformatics, AgTech), including feature engineering from omics data, biomarker discovery, predictive modeling, and deployment-ready datasets/pipelines.

Organisms & systems we've worked with

Bacteria and plasmids, including deep expertise in the Bacillus subtilis group and Bacillus cereus group, with published work on taxonomy across related species.

Yeasts and fungi, including Komagataella phaffii, Pichia pastoris and Trichoderma.

Mixed microbial communities (microbiomes), especially from soil and natural environments.