Transcriptome Annotation

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.

Expertise:

Igenbio, Inc. develops genome analysis products and services for the life science industry. Our scientists have broad experience in both in silico and wet lab sequencing, research and development with more than 100 relevant publications in these areas. Igenbio has a proven track record of delivering scientific results for academic, governmental, and industrial institutions for two decades.

Our expertise includes, but is not limited to:

• Whole Genome Sequencing
• RNA-Sequencing
• Metatranscriptomics Sequencing
• Metagenome Sequencing
• Common and custom amplicon sequencing
• Genome Assembly & Annotation
• RNA-Seq Analysis
• Amplicon Sequencing Analysis
• Metagenome Analysis
• Genome ORF calling: Eukaryotes and Prokaryote Genomes
• Pathway Analysis
• Metabolic Reconstruction
• SNP Discovery & Analysis
• Comparative Genomics
• Available for all organisms, including humans, animals, plants, bacteria, and viruses.
• Haploid, diploid or polyploid assemblies

Infrastructure:

Igenbio has a large, secure cloud infrastructure that can expand to meet any project demands you may have - from large number of samples to quick turnaround times. Please inquire for more information.

At Igenbio, Inc. security of your data is a top priority. Your data is protected by best practices in physical and data security measures. This includes 24/7 physical security and monitoring, and the best available encryption for storage and transmission. Our employees are trained and knowledgeable in data security best practices.

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.

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.

Minnesota Informatics specializes in the analysis of genomic and expression data for reference and non-reference species. We are experienced in the QC, mapping/assembly, quantification and evaluation of NGS data for RNA-Seq, SNP and Single Cell sequencing projects. We have worked with human and model mammal organisms as well as plant and bacterial genomes.

We distill the large NGS datasets down to manageble tables and graphics of significant, differentially expressed or variant genes/loci.

World Fusion is a well-established bioinformatics and cheminformatics software developer and services supplier with offices in Japan and the US. We have been at the forefront of developing genomic and drug discovery research tools since our early work on the Human Genome Project, and offer unparalleled reliability and expertise in our services.

Our customizable services include NGS data analysis, in-silico research services, and we are annotation specialists offering the most comprehensive correlations between genes, proteins, diseases, and chemicals.

The majority of the information is generated from our proprietary genomic and drug discovery research platform and knowledge base that we have been upgrading and building upon for over 10 years. It is comprised of original in-house data, curated information from over 60 top public data sets, and a chemical dictionary containing over 75 million non-redundant chemical compounds.

Our more recently added metagenomic and metaranscriptomic analysis services are carried out using state-of-the-art, original in-house software applications.

We offer MANY additional services, please contact us about your specific needs.

ContigExpress is the leading integrated genomics data service provider. We offer genomic project management, data analysis, and bio-IT consulting services. Our unique value to our clients lies in our deep understanding of both biology and informatics. From project consultation, bio-IT infrastructure implementation, to data analysis, our experienced scientists deliver not only cost-effective customized informatic solutions but also their expert insights.

Our team consists of Ph.D.-level computational biologists with extensive training and professional practice in bioinformatics and genomic research. We understand both your cutting-edge research and your informatics challenges. We enable you and your team to extract actionable information from the vast amount of genomic data in a cost-effective and timely fashion.

We at ContigExpress strive to deliver affordable expert genomic data solutions to researchers and clinicians. We place the utmost emphasis on information confidentiality, data security, and data integrity. Please schedule a complimentary project discussion with one of our expert bioinformaticians to discover how we can help you move your genomics research forward!

DATA ANALYSIS Routine NGS data analysis in the area of genomics and transcriptomics, such as: - Gene expression and differential expression analysis - De novo and ab initio transcriptome assembly - Small RNA analysis - Genome variant calling and annotation

Customized tasks, including: - Identification of long noncoding RNAs - Identification of ta-siRNAs - Isomir and miRNA editing analysis - Annotation of non-model organisms - Building transcriptome-wide maps of RNA-RNA interactions

WORKSHOPS We offer workshops in a broad spectrum of bioinformatics applications, including: - RNA-Seq data analysis (4 days) - NGS in medical research (4 days)

EXPERIENCE We’ve been in the market since 2013 and came into collaboration with hundreds of customers. We’ve been working on model and non-model organisms, including viruses, bacteria, fungi, plants, animals, and human. We are part of research consortium aiming at development of personalized medicine services for diagnosis and treatment of lung cancers. We are also actively conducting research projects in different areas of genomics and transcriptomics, which gives us expertise in standard and up-to-date bioinformatics solutions.

INFRASTRUCTURE We have access to dedicated file storage and computational servers, with virtually unlimited (on demand) capacity.

Dreamgenics is a biotech company that offers bioinformatics analysis services for genomic, transcriptomic and metagenomic NGS data using our Genome One software. Genome One (CE-IVD certified) is an advanced tool that allows the integration of all the bioinformatics solutions required for the study, including read alignment, variant calling and annotation. Our analyses identify high-quality genomic variants through high sensitivity and specificity standards, extracting important biological information and reducing validation costs. The services that we offer are the following: WGS, WES, Gene panels, Transcriptomics (RNA-Seq) and Metagenomics. Additionally, we hand in the results using our web viewer Genome One Reports (https://www.dreamgenics.com/en/genome-one/).

The use of our bioinformatics tools allows us to offer you high-quality results in a fast and simple way. By using our analysis services, you considerably reduce costs and the investment in technological devices, informatics and qualified professionals.

Lastly, we are an ISO 9001:2015, UNE-EN ISO 13485:2018 and UNE-ISO/IEC 27001:2017 certified company which represents our commitment to provide our customers with products and services that meet the most demanding quality standards.

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

• End-to-end diagnostics services featuring whole genome sequencing - for clinical applications of cancer, rare disease and MRD. Below are the listed applications for research:

Biopharmaceuticals and biotechnology --- Identify candidate biomarkers that correlate with outcomes Understand responders vs. non-responders during or post clinical trials Accelerate clinical trial enrollment by identifying patients for rare indications Analyze clinical trial results for efficiency and safety profile Leverage genetic information for label expansion with real world data Provide genetic testing for patient support program

Biobanks, research organizations and labs --- Research genomic profiles in-depth, often resulting in new biomarker identification, or re-classification Profile genomic characteristics of the acquired biospecimen to increase the value of your biospecimen assets

Health technology --- Leverage genetic information to provide precision health insights to your customers and users Generate real world evidence data including genetic information

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.