Read Filtering and Cleaning

The OMRF Genomics facility is a universally accessible resource able to provide investigators with massive amounts of sequencing, genotyping, or gene expression data in a relatively short period of time. Our NovaSeq X Plus and NextSeq 2000 instruments combine to provide researchers extreme flexibility in a very cost-efficient manner.

VIB Nucleomics Core started off in 1999 as the VIB MicroArray Facility (MAF), a service facility to provide expert services in expression analysis. In the early days, in-house developed and spotted arrays were used in addition to arrays from commercial providers. With commercial providers improving on array quality and offering custom array content, the microarray facility stopped producing its own arrays in 2008. It was decided to broaden the spectrum of platform technologies offered to the life science community. Since then the facility is offering expert services in nCounter technology and sequencing. To reflect this expanded portfolio, the microarray facility was renamed to VIB Nucleomics Core, reflecting the (bioinformatic) analysis of both RNA and DNA. The latest addition to the portfolio of technologies offered is genome mapping from BioNano Genomics.

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.

Bioinformatics Services for Plant Scientists and Breeders by Computomics

At Computomics.com, we deliver in-depth NGS analyses. We start by identifying your breeding or research goals, devise a sequencing strategy to achieve them and define the project deliverables and timeline through an initial consultation. Our methods include the latest algorithms from the bioinformatics community.

We protect the security of your data. We use high-performance servers in a high-security data center with two-factor access control mechanisms. During the analysis, we use transparent, reliable processes and quickly deliver highly reproducible results in constant feedback with you, via virtual or onsite meetings at your location.

Our NGS products are exclusively focusing on plant species and their interacting microbes, and include: 

• Reference genome assembly: experience with polyploids and genomes up to 22 Gbp
• Genome annotation: ab initio gene and transcript isoform prediction, protein function, ncRNA annotation
• Genomic variance analysis and comparison: for marker development, phylogenetic studies, and comparative genomics
• Bulk segregation analysis, genotyping, marker development
• Differential gene expression, de novo transcriptome assembly
• World’s fastest, most accurate metagenomics
• Statistically sound epigenetics
• Genomic selection with continuous model improvement

Computomics collaborates with world-leading scientists, opening up an unprecedented opportunity for breeders and plant scientists. We provide data of the highest possible quality that expedite your crop improvement programs.

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.

Beckman Coulter Genomics offers next generation sequencing services designed to meet the evolving sequencing needs of academic, biotechnology and pharmaceutical researchers worldwide. A comprehensive range of next generation sequencing services is available utilizing platforms from Illumina and Roche.

End to end solutions are offered allowing tailoring of projects to your specific needs. A wide variety of bioinformatics packages are available and results consultation is provided to ensure you understand the data returned to you. For the quickest service we accept pre-made libraries for sequencing only projects.

• Expert scientists consult on project design to ensure appropriate experimental approach • Beckman Coulter instrumentation utilized for fully automated library construction and target enrichment with enhanced reproducibility and reliability • Bioinformatics scientists oversee all data analysis to ensure quality
• Videoconference provided for report review and results discussion

Trusted Partner • Over 20 years sequencing experience • 1,500+ customer publications • 200+ successful audits • Experienced staff from well-known institutes of academic and commercial excellence • Contributed sequencing data to • >10 genome projects including mouse, cat, dog and salmon • >100 Microbial and Fungal genomes

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.

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.

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.

TAGCC is an African company offering services in next generation sequence data analysis and consultancy in genomics. We have implemented a wide range of pipelines to analyse NGS data from various platforms including Illumina and 454. We support design and implementation of genomics and NGS based projects.

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.

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.