--- title: "Plant and Animal WGS" search_description: "IGATech offers specialized whole genome sequencing for plant and animal genomes, delivering high-quality, comprehensive data for agricultural, ecological, and genomic research. Optimize your research with our advanced sequencing solutions." published: 2024-11-10 22:07:30.042702+00:00 locale: "it" --- # Plant and Animal WGS [Request a quote](https://igatechnology.com/igatech/contacts/#contact-form) ## Technologies ![NovaSeq X Plus](/media/images/Illumina_NovaSeq_XPlus_Left_561x375.width-500.png) ### NovaSeq X Plus The NovaSeq X Plus is a powerful and scalable ultra-high-throughput sequencing system that supports the broadest range of applications and study sizes. Unrivaled data quality using Illumina's proven SBS chemistry has made the NovaSeq X Plus the instrument of choice for all major genome centers and leading institutions throughout the world. Producing up to 25 billion reads \(7.5 Tbp\) per flowcell, yielding up to 120 human genomes in about 2 days at full capacity. ![Whole Genome Sequencing](/media/images/Whole_genome_sequencing.width-500.png) ### Whole Genome Sequencing The whole genome sequence as the most comprehensive overview of its composition. Identify most of the variability accounted by SNPs, CNVs, PAVs, insertions, deletions, translocations along with its functional impact on the genetic code an organism. Dedicated technologies are applied for *de novo* reconstruction of personal genomes to an affordable price, providing an unbiased method to depict each individual human \(and non-human\) genome. See [*de novo*](https://igatechnology.com/genomics-research-services/?area=plant#denovo) - [whole genome resequencing](https://igatechnology.com/genomics-research-services/whole-genomics-resequencing/). ![Low-pass sequencing](/media/images/low.width-500.png) ### Low-pass sequencing An alternative way to pursue genotyping/classification experiment is carried to a very low coverage per individual. This technique is adopted in several applications such as metagenomics, allele/SNP mining, Pop-Seq, Pool-Seq. Haplotype/organism identification will rely on a ‘horizontal’ coverage rather than a ‘vertical’ coverage. This analysis does not have sufficient information to detect structural variation, but dramatically reduces costs in large genotyping and metagenomics experiments. See [metagenomics](https://igatechnology.com/genomics-research-services/plantanimal/metagenomics/) - [bioinformatics](https://igatechnology.com/bioinformatics-support/) ![AVITI Element Biosciences](/media/images/0.width-500.png) ### AVITI Element Biosciences The AVITI System by Element Biosciences is a benchtop sequencer designed for high performance, cost efficiency, and flexibility. It features dual independent flow cells for parallel or independent operation, enabling flexibility in throughput from low to full. The system utilizes Avidity Sequencing™ technology, ensuring over 90% of reads exceed Q30 quality, with minimal errors, low duplication rates, and reduced AT/GC bias. It supports easy data conversion to FASTQ files, offers compatibility with numerous assays, and provides cost-effective sequencing. This is our ideal companion for dedicated and fast-turnaround run set-up. For more detailed information, you can visit their website directly at [https://www.elementbiosciences.com/products/aviti](https://www.elementbiosciences.com/products/aviti). ![Nanopore Sequencing](/media/images/1.width-500.jpg) ### Nanopore Sequencing Nanopore sequencing is empowering many applications by the ability to analyze DNA, RNA and their modifications with no limitation on sequence length. This is of particular importance when the goal is to resolve hard-to-sequence or repetitive regions that have so far hampered the possibility to decode structural and epigenetic variation. Also, direct RNA sequencing and full-length cDNA sequencing are providing unprecedented insight into the real strucure and abundance of transcripts isoforms. ## One size does not fit all 1. Full-coverage whole genome sequencing 2. Low-pass whole genome sequencing 3. Long-read genome sequencing 4. Adaptive sampling Nanopore sequencing ## Most requested applications 1. Comparative genomic analysis 2. Identification of somatic and germline structural variants 3. Identification of germline and somatic SNPs. 4. Clonal fingerprinting and parental testing for variety protection 5. Identification of chromosomal abnormalities 6. Insertion analysis \(transposable elements\) 7. SNP and SV phasing 8. Methylation phasing ## All genetic tests in one **HIGH-RESOLUTION BASE-BY-BASE VIEW OF THE GENOME** Captures both large and small variants that might otherwise be missed Whole genome sequencing \(WGS\) in plants and animals opens a new frontier in genomics, offering transformative possibilities across various fields such as agriculture, breeding, research, and ecology. This comprehensive approach surpasses traditional array-based solutions by providing a depth of information and versatility that can revolutionize how we understand and manipulate the genetic basis of life. - **Farming and Agriculture** - **Animal Breeding** - **Plant Breeders and Researchers** - **Ecology and Conservation** ![chromosome-wise-SNPs](/media/images/chromosome-wise-SNPs.width-1500.png) SNP distribution along chromosomes can be used to infer kinship and define pattern of haplotype sharing to shed light on the pedigree of varieties. **Complete Coverage WGS**: This method provides an exhaustive view of the genome, capturing every region with high fidelity. It is ideal for comprehensive genetic analysis, allowing for the detection of both common and rare genetic variants. Complete coverage is essential in clinical research and diagnostics where a detailed understanding of the genetic makeup is crucial for identifying pathogenic mutations and tailoring personalized treatments. **Low-Pass WGS**: By sequencing the genome at lower coverage, low-pass WGS offers a cost-effective solution for studies requiring a broad overview rather than detailed variant analysis. This approach is suitable for population genetics and large cohort studies, where the goal is to identify common genetic patterns and associations rather than detailed genotypes of each individual. **Long Reads \(Nanopore\)**: Nanopore sequencing provides long reads that can span thousands of base pairs, making it exceptionally useful for characterizing complex regions of the genome, such as structural variants and repetitive sequences. This technology shines in research areas where resolving complex genomic architectures is necessary, such as in the study of genomic rearrangements in cancer or in comprehensive genome assembly projects. **Adaptive Sampling \(Nanopore\)**: This advanced feature of Nanopore sequencing technology allows selective sequencing of specific genomic regions of interest. By enriching for particular areas, adaptive sampling makes it possible to focus sequencing efforts and depth where it is most needed, enhancing both cost-efficiency and analytical precision. This approach is particularly beneficial in targeted studies, such as those focusing on specific genes known to be involved in disease, or in regulatory regions critical for gene expression studies. We also offer DNA extraction sample preparation service and provide full support on study design to ensure correct sequencing and bioinformatics strategies are used to meet your project goals. Our expert will consult with you about your specific requirements. ## IGATech Sequencing Services Our workflow begins with purified genomic DNA or we can provide a dedicated nucleic acids extraction service \(please enquire for accepted tissues\). PCR-based or PCR-free library preparation can be used to generate libraries. Sequencing can be performed on one of the following platforms: - Illumina NovaSeq - Element Biosciences AVITI - Oxford Nanopore PromethION Several QC steps are performed during the sample processing ensuring the delivery of the highest quality data available. ### ## Bioinformatics Analysis **Genome resequencing - standard bioinformatic analysis includes:** - Alignment to reference sequence - Quality control and improvement of reads - Variant calling \(germline SNP, indels, SVs\) - Coverage statistics and metrics **Genome resequencing - advanced bioinformatic analysis includes:** - Identification of somatic structural variants - Identification of somatic SNPs. - Clonal fingerprinting and parental testing for variety protection - Identification of chromosomal abnormalities \(karyotype testing, aneuploidy, chimeric somatic variants\) - Event-specific insertion analyses #### ![P24-light](/media/images/P24_FP5WKtp.width-1500.png) #### Oxford Nanopore: delivering of **phased SNPs**, **structural variants** and **methylation profiles in a single experiment** ![ONT-meth](/media/images/ONT-meth.width-1500.png) Haplotype-resolved structural variation \(Copia-like transposable element insertion on track 1\) and associated variation in the methylation pattern ### Are you ready to move your genome biology research to the next level? ## Documents & Reports - [Privacy Information.pdf](/documents/12/Privacy_Information_rev00.pdf) - [Human samples clearance.pdf](/documents/13/__Human-samples_clearance.pdf) - [Shipping and Packaging Guidelines.pdf](/documents/9/SHIPPING_AND_PACKAGING_GUIDELINES.pdf) - [rev05 Terms and Conditions.pdf](/documents/137/__M12_01_rev05_Terms_and_Conditions.pdf)