De Novo Genome Sequencing of plants, animals and insects

Welcome to Nucleome: India’s Premier De Novo Genome Sequencing Service Provider

At Nucleome, we take immense pride in being India’s exclusive service provider of Whole-genome sequencing and hybrid assembly using the state-of-the-art Illumina NovaSeq 6000 and PacBio Sequel II technologies. When it comes to sequencing the genomes of diverse organisms, our expertise and cutting-edge approaches set us apart.

Unraveling the Genomic Secrets with PacBio Sequel II:

To ensure accurate and high-quality genome sequencing, we leverage the power of PacBio Sequel II, along with optical mapping and Hi-C approaches. Our accomplished team has successfully completed genome sequencing and assembly projects for a wide range of organisms, including microbes, fungi, plants, insects, and animals, using Illumina NovaSeq 6000 and PacBio Sequel II. Irrespective of your sample type and budget, our experienced professionals can customize a suitable strategy for your specific project needs. Explore our PacBio Sequel II service page for more detailed information.

Leading the Way in Vertebrate Genome Sequencing:

Nucleome stands as the most proficient team in India for sequencing vertebrate genomes. In collaboration with the Vertebrate Genomes Project (VGP), we are actively working with Indian researchers to sequence 100 vertebrate genomes from India. This groundbreaking initiative showcases our commitment to advancing genomics research and conservation efforts in the country.

Achieving Exceptional Genome Assemblies:

When it comes to attaining the highest-quality genome assemblies, we rely on PacBio Sequel II data, scaffold with Bionano datasets, and apply Hi-C technology to build chromosome-level scaffolds. Our meticulous assembly assessment and curation processes ensure scientists receive error-free scaffolds from the available datasets. Notably, our portfolio includes the successful sequencing of genomes such as the Tiger, Great Indian Bustard, Mango, Pigeon Pea, Pomegranate, Mithun, and numerous microbial and fungal genomes.

At Nucleome, we leave no stone unturned in achieving the most comprehensive and accurate genome assemblies. Our cutting-edge pipeline commences with reference-free genome profiling using k-mers, providing us with valuable insights into the genetic landscape of the organism under study. Leveraging the power of HiFi reads, we expertly assemble contigs using hifiasm, while also incorporating additional phasing data if available. This meticulous approach ensures that we capture the intricate genomic structure with high precision.

Quality Control and Purging for Pristine Contigs

In our pursuit of excellence, we place immense emphasis on quality control. Our expert team diligently detects and identifies false duplicates during this crucial step. Should any be detected, the contigs undergo a thorough purging process to remove any inaccuracies, ensuring that only the most reliable genetic information is retained.

Scaffolding with Optical Maps and Hi-C Data

Taking the process further, we engage in meticulous scaffolding, a critical phase in the de novo genome assembly. For enhanced accuracy and completeness, we utilize optical maps when available, shedding light on the long-range order of DNA fragments. Additionally, we harness the power of Hi-C data, which reveals valuable insights into the spatial organization of the genome. This combination of technologies results in robust and contiguous genome structures.

Decontamination for Pristine Genomes

As part of our unwavering commitment to providing the highest-quality genome assemblies, a final decontamination step is conducted. This critical stage ensures that any potential contaminants are meticulously removed, leaving us with genomes that are pure and untainted.

Exemplary De Novo Genome Assembly

At Nucleome, we pride ourselves on delivering exemplary de novo genome assemblies, unravelling the genomic mysteries of diverse organisms with utmost precision. Through our cutting-edge pipeline and expert team, we provide you with comprehensive and accurate genomic data, opening doors to endless possibilities in genomics research.

Your Partner in Genomics Research:

At Nucleome, our dedicated team is here to assist you at every step of your project. From designing the ideal project plan and selecting the most suitable technology to expertly executing sequencing and conducting comprehensive analysis, we are your trusted partners in genomics research. Feel free to reach out to our team at +91 40 4011 4169 or send a query to info @ nucleomeinfo.com.

Join us on this thrilling journey of discovery, and let our unparalleled expertise and advanced technologies empower your genomics research. Whether you are studying microbes, fungi, plants, insects, or animals, we stand ready to assist you in achieving exceptional genome assemblies and unlocking the secrets of life.

Optical Mapping

Optical mapping is a molecular technique that produces fingerprints of DNA sequences in order to construct genome-wide maps. The sequence markers can be ordered restriction fragments, or specific sequence motifs (nick sites). The optical mapping procedure first stretches relatively intact (minimally-sheared) linear DNA fragments on a glass surface or in a nanochannel array, and then directly images the locations of the restriction sites or sequence motifs under light microscopes, with the aid of dye or fluorescent label. Optical mapping has been widely used to improve de novo plant genome assemblies, including rice, maize, Medicago, Amborella, tomato and wheat, with more genomes in the pipeline. We use Bionano Irys system to offer optical mapping service that provides long-range information of the genome and can more easily identify large structural variations. The ability of optical mapping to assay long single DNA molecules nicely complements short-read sequencing which is more suitable for the identification of small and short-range variants.

Optical Map guided genome assembly

There are several ways in the assembly process that optical mapping can assist in building high quality reference genomes. De novo constructed optical maps offer independent evidence to connect and bridge adjacent sequence contigs or scaffolds. Genome assemblies guided by optical maps consist of three key computational steps. The initial step is the de novo assembly of optically mapped molecules to construct a ‘consensus’ optical map from single DNA molecules at high redundancy. The consensus map has to deal with errors specific to optical mapping including missing cuts, false cuts, inaccurate fragment sizes, and chimeric maps. The next step is to align the in silico digested contig sequences to the consensus optical map. The final step is the joining of neighbouring contig sequences to construct supercontigs on the basis of their locations on the optical map. For small microbial genomes, the resulting assemblies could contain a single extent of sequence that spans the entire genome, while for large eukaryotic genomes the combined efforts of sequencing and optical mapping often result in substantially increased scaffold N50. In several cases, the mapping data allow the reconstruction of entire chromosomes. Beyond ordering and orientating contigs, optical maps provide an additional layer of validation to the sequence assemblies. Optical maps could potentially identify and resolve misassemblies – false joins, inversions or translocations that are artifacts, which occurred during the sequence assembly.

Whole Genome Resequencing

Plant and Animal Genome Resequencing:

Whole genome re-sequencing approach can be used to the underlying mechanisms of species origin, development, growth, and evolution. Using Whole Genome Resequencing, the complete genome data from one or more variants can be aligned to the known reference genome of the species. Applications of WGS include the detection of genetic differences between variants, transposon fingerprinting for assessing germplasm diversity and lineages, and mapping loci associated with specific traits, such as disease resistance.

Resequencing plant and animal genomes holds immense significance in modern genomics research. Here are some key reasons why resequencing these genomes is essential:

1. Genetic Diversity and Evolution Studies: By resequencing plant and animal genomes, researchers can gain insights into genetic diversity and understand evolutionary processes. This information is crucial for conserving biodiversity, crop improvement, and understanding species adaptation to changing environments.
2. Identification of Genetic Variants: Resequencing helps identify genetic variants, including SNPs, CNVs, and InDels. These variants play critical roles in determining phenotypic traits, disease resistance, and other important characteristics.
3. Genome-Wide Association Studies (GWAS): Resequencing data enables GWAS, which helps researchers associate genetic variants with specific traits or diseases. GWAS can unravel complex genetic interactions and facilitate targeted breeding or medical interventions.
4. Marker-Assisted Breeding: Resequencing allows the discovery of high-quality genetic markers linked to desired traits in plants and animals. These markers aid in accelerating traditional breeding programs, leading to the development of improved varieties with desired traits.
5. Comparative Genomics: Resequencing multiple plant and animal genomes enables comparative genomics, revealing evolutionary relationships and evolutionary dynamics. This approach is particularly beneficial for understanding gene family expansions, genome rearrangements, and species divergence.

Nucleome’s Extensive Research Experience in Genomics:

With over ten years of extensive research experience in the field of genomics, Nucleome Informatics has established itself as a trusted leader in genetic sequencing and data analysis. Our rich experience, backed by a track record of processing more than 50,000 samples, makes us the ideal partner for your genomics research needs.

How Nucleome Assists Researchers in Obtaining High-Quality Genetic Markers:

1. Advanced Sequencing Technologies: Nucleome employs state-of-the-art sequencing platforms, such as the Illumina NovaSeq 6000, for generating high-quality, accurate, and reliable sequencing data.
2. Expert Bioinformatics Analysis: Our experienced bioinformatics team uses sophisticated algorithms and pipelines to analyze sequencing data. We identify genetic variants, perform advanced analysis, and provide comprehensive annotations, ensuring you obtain high-quality genetic markers.
3. Comprehensive Sample Processing: Nucleome caters to a diverse range of sample types, including plants and animals. Our expertise in handling different sample types ensures accurate and meaningful results for various applications.
4. Tailored Solutions for Specific Applications: Whether you are conducting research in agriculture, biodiversity, animal genetics, or human health, Nucleome offers tailored solutions to meet your specific research objectives.
5. Collaborative Approach: At Nucleome, we value collaboration with researchers and scientists. Our team works closely with you to understand your research goals and provide personalized support throughout the project.
6. Data Interpretation and Insights: Beyond data analysis, Nucleome assists researchers in interpreting results and drawing meaningful insights from the genetic markers identified through resequencing. Our expertise adds value to your research findings.

Partner with Nucleome Informatics:

As a pioneer in genomics research, Nucleome Informatics is committed to empowering researchers with high-quality genetic markers for diverse applications. Collaborate with us to leverage our expertise, advanced technologies, and years of experience in genomics to advance your research and make significant contributions to the scientific community. Together, let’s unlock the potential of resequencing plant and animal genomes and drive innovation in the world of genomics research.

Microbial Genome Resequencing- Accurate Reference Generation and Comparative Genomic Studies:

Our Microbial Whole Genome Sequencing service is tailored to accurately sequence and compare microbial genomes. Key features of this service include:

• Comparative Genomic Studies: We conduct comparative analysis of multiple reference genomes to mapped genomes of new organisms, facilitating accurate microbial identification and evolutionary research.
• Time- and Cost-Effective: Unlike conventional approaches like PCR, Whole Genome Sequencing eliminates labor-intensive cloning and mapping steps, making it a time- and cost-effective solution.
• High-Throughput Sequencing: Our high-throughput sequencing approach enables the simultaneous sequencing of numerous microbial samples through multiplexing.

Applications of Microbial Whole Genome Sequencing:

• Detection of Variations within Target Genomes: Our service allows for the detection and analysis of genetic variations within microbial genomes, providing insights into microbial diversity and evolution.
• Character Differences Interpretation: We aid in the interpretation of character differences between microbial strains, aiding in the understanding of their functional implications.
• Large-Scale Evolution Research: By generating accurate reference genomes and conducting comparative genomic studies, we contribute to large-scale evolutionary research.

Data Analysis for Microbial Genome:

Our Microbial Whole Genome Sequencing data analysis includes the following components:

• Data Quality Control: We ensure data quality by filtering reads containing adapters or with low quality, ensuring reliable results.
• Alignment with the Reference Genome: We accurately align the clean reads to the respective reference genome, allowing for precise variant calling.
• Statistics of Sequencing Depth and Coverage: We provide detailed statistics on sequencing depth and coverage to assess the genomic representation.
• SNP/InDel Calling, Annotation, and Statistics: We identify SNPs and Indels, and provide annotations and statistical insights to interpret genetic variations.
• CNV Calling, Annotation, and Statistics: We detect Copy Number Variations and offer annotations and statistical analysis, providing valuable insights into genomic structural variations.
• SV Calling, Annotation, and Statistics: Our advanced analysis includes the detection of Structural Variants, contributing to a deeper understanding of microbial genome architecture.

At Nucleome Informatics, we are your trusted partner for Whole Genome Resequencing, providing specialized analysis for plant, animal, microbial, and human genomes. Collaborate with us to uncover the mysteries within your genomes and drive groundbreaking discoveries in genomics research.

Human Genome Resequencing

Nucleome offers highly precise, inclusive human whole-genome sequencing services, giving researchers, Physicians and patients the clearest picture of the genome using the advanced genome sequencers available at Nucleome’s human genomics lab called DrSeq Labs (www.DrSeq.com).

For whole genome sequencing, we extract DNA from blood or tissue and then determine the identity of the 3 billion nucleotides that compose the human genome. Today, most genetic testing focuses on one or a few genes, rather than the entire genome. However, with the availability of human genome sequencing service in India at Nucleome Informatics, now more individuals are pursuing this option. Physicians can look at an entire genome to see how specific treatments for a disease will be affected by an individual’s unique genome. For example, the physician may opt to look at genes involved in drug metabolism when deciding dosage. In the future, whole genome sequencing may enable everyone to develop a personalized treatment plan.

Advantages of Whole Genome Sequencing

• Creating personalized plans to treat disease may be possible based not only on the mutant genes causing a disease, but also other genes in the patient’s genome.
• Genotyping cancer cells and understanding what genes are misregulated allows physicians to select the best chemotherapy and potentially expose the patient to less toxic treatment since the therapy is tailored.
• Previously unknown genes may be identified as contributing to a disease state. Traditional genetic testing looks only at the common “troublemaker” genes.
• Lifestyle or environmental changes that can mediate the effects of genetic predisposition may be identified and then moderated.

Sequencing Strategy

• 350 bp insertion DNA library.
• Illumina HiSeq Platform, Paired-end150 bp.
• Sample Requirements.
  • DNA amount quantified by Qubit 3.0
  • For fresh sample: ≥2.0 μg (for two libraries prep); minimum: 500 ng
  • For FFPE sample: ≥3.0 μg (for two libraries prep); minimum:1μg
  • DNA concentration: ≥20 ng/μL
  • Total volume: ≥10 μL
  • Purity: OD260/280= 1.8-2.0 without degradation or RNA contamination
  • Turnaround Time: Within 45 days from sample verification Additional 15 days for standard bioinformatics analysis
• Recommended Sequencing Depth
  • For normal sample: effective sequencing depth 30X
  • For tumor sample: effective sequencing depth 50X

Bioinformatic Analysis

• Data quality control: filtering reads containing adapter or with low quality
• Alignment with reference genome, statistics of sequencing depth and coverage
• SNP/InDel/SV/CNV calling, annotation and statistics
• Somatic SNP/InDel/SV/CNV calling, annotation and statistics (paired tumor samples)

For more information please visit our website www.DrSeq.com;

If you are interested to sequence your genome and need more information, please write to us at info @ drseq.com.

DrSeq Exome Sequencing

DrSeq Exome Sequencing Service: Advancing Genomics with Unparalleled Precision

Welcome to Nucleome Informatics, where cutting-edge genomics research meets excellence in Exome Sequencing. We are thrilled to present our latest innovation, the DrSeq Exome Sequencing Service, designed to empower researchers with unprecedented insights into the human genome. As India’s most trusted brand in genomics, we are committed to delivering top-notch solutions tailored to your specific research needs.

Unleashing the Power of DrSeq Exome Sequencing

At Nucleome Informatics, we understand the importance of unraveling the mysteries hidden within the protein-coding region of the human genome – the key to understanding disease-related variants. DrSeq Exome Sequencing is our state-of-the-art service, offering a cost-effective and comprehensive solution to accelerate your genomics studies.

Why Choose DrSeq Exome Sequencing Service?

Comprehensive Coverage:

DrSeq Exome Sequencing is carefully engineered to capture the entire protein-coding region of the human genome. Our approach ensures a holistic analysis of crucial variants, providing you with an extensive view of the genetic landscape and uncovering novel insights.

High-Quality Data:

We employ the Roche Kapa Hyper Exome Kit for exome capture, complemented by the advanced Illumina NovaSeq 6000 for sequencing. This powerful combination guarantees that ≥ 85% of bases have a sequencing quality score ≥ Q30, surpassing Illumina’s official guarantee of ≥ 75%. With DrSeq Exome Sequencing, you can trust in the accuracy and reliability of your data at every step.

Exome Sequencing Applications:

DrSeq Exome Sequencing service caters to a diverse range of genomics applications, including:

SNV/Indels Discovery:

Unleash the power of unparalleled precision as you identify Single Nucleotide Variants (SNVs) and small insertions/deletions (Indels). Discover subtle genetic changes crucial for understanding disease development.

Copy Number Variation Discovery:

Explore the depths of genetic complexity with in-depth analysis of copy number variations (CNVs). Our service helps unravel the intricate genetic architecture underlying various diseases.

Trio Analysis:

Leverage the potential of Exome Sequencing on related individuals (trios) to investigate Mendelian inheritance patterns. DrSeq Exome Sequencing aids in uncovering hereditary diseases within families.

Exome Capture Kits:

Select from our esteemed Exome Capture Kits tailored to meet your research requirements:

Introducing the KAPA HyperExome Probes: Roche’s Advanced Whole Exome Sequencing Solution

We are delighted to announce the inclusion of the KAPA HyperExome Probes in our Exome Capture Kits lineup. Developed by Roche, this cutting-edge solution incorporates next-generation KAPA Target Enrichment Probe technology. The KAPA HyperExome Probes offer broad and relevant database coverage, enhanced sequencing efficiency, and increased coverage in hard-to-sequence regions. With its actionable and well-annotated content, this ~43 Mb capture target size includes 387 sample tracking SNPs, streamlining sample identity tracking throughout the WES workflow.

Features and Benefits of KAPA HyperExome Probes:

• Uncover difficult regions and access more content from essential genomic databases.
• Validated with the KAPA HyperCap Workflow v3.0, ensuring high sequencing efficiency with superior uniformity and low duplication rates.
• Achieve higher result confidence with >98.7% sensitivity and >99.7% specificity of SNP detection.
• Strengthened enrichment by high fidelity probes manufactured with KAPA HiFi DNA Polymerase, targeting both DNA strands.
• Intrinsically target 387 sample tracking SNPs for streamlined sample identity tracking.

Data Analysis: Unveiling Insights with Precision

At Nucleome Informatics, we offer both standard and advanced data analysis options to unlock valuable insights from your sequencing data. Our expert team delivers:

Standard Data Analysis includes:

• Variant Calling (SNPs/InDels) & Annotation: Accurate identification of Single Nucleotide Polymorphisms (SNPs) and small insertions/deletions (InDels) with comprehensive annotation.

Advanced Data Analysis includes:

• CNV (Copy Number Variation) Analysis: In-depth exploration of copy number variations, vital for cancer research, family analysis, and population studies.
• Various Variant Calling Pipelines: Customized pipelines tailored to your specific research objectives.
• Cancer Analysis / Family Analysis / Population Analysis: Tailored analysis for cancer studies, family-based genetic investigations, and population genetics research.

Custom Sequencing and Bioinformatics Analysis:

Recognizing the uniqueness of every research project, we offer custom sequencing and bioinformatics analysis services. Our experts perform data QC, mapping with the reference genome, SNP/InDel calling, statistics, and annotation to unlock the full potential of your data.

Special Panel Development: Advancing Genomics Research in India

Our commitment to advancing genomics research in India is exemplified by our ongoing development of a specialized panel for Inherited Retinal Diseases. Designed to cater specifically to the Indian population, this initiative aims to impact healthcare outcomes positively.

Sample Conditions: Accuracy at the Forefront

To ensure the utmost accuracy in your results, please provide the following sample conditions:

• DNA amount: 1μg or more, volume: 20μl or more, concentration: 20ng/μl or more
• FFPE amount: 1.5μg or more

Collaborate with Us: Empowering Your Genomics Research

At Nucleome Informatics, we are more than just a service provider; we are your reliable partner for high-quality, affordable, and convenient Exome Sequencing. Whether your research focuses on rare Mendelian disorders, complex diseases, cancer studies, or human population research, our DrSeq Exome Sequencing Service is designed to meet your unique needs.

Contact us today to collaborate on your next groundbreaking genomics study and unlock the secrets hidden within your data. Together, let’s push the boundaries of scientific discovery with the precision and power of DrSeq Exome Sequencing Service.

Single Cell DNA Sequencing

The genomic heterogeneity of cell populations can be explored at the level of the individual cell. Genetic changes, such as point mutations and copy number variation occurring during disease and normal development processes, are profiled using the minute amounts of DNA from single cells. Applications include analysis of genetic heterogeneity within unicellular and multicellular organisms, detection of chromosomal anomalies in germ line cells, preimplantation genomic screening of embryos, and defining the genetic composition of tumors for developing more targeted therapies.

The single cell DNA sequencing service includes sample QC, amplification, library preparation, sequencing and bioinformatics analysis. We use the MALBAC (multiple annealing and looping based amplification cycles) PCR-based method, which provides uniform data while reducing rates of false positives and false negatives.

Genotyping By Sequencing

This application is used to compare genotypes through the mapping of large numbers of SNPs or other markers. Genotyping by sequencing (GBS) is a rapid and cost-effective approach which uses a restriction enzyme digestion step to reduce genome complexity, so GBS can be applied to large genomes, and the end reads of the restriction fragments allow variants to be compared when no reference genome is available.

Applications of genotyping by sequencing include tracking plant and animal genotypes in breeding programs and conservation projects, examining the diversity of natural populations, discovery of new genetic markers, and screening variants prior to whole genome re-sequencing.