Bioinformatics
Variant Analysis
Variant Analysis
Long-read sequencing data affords the most comprehensive look at the genome and reveals variants that are unable to be detected using short reads. In addition to single-nucleotide variants (SNVs), long-read data allows for the discovery and exploration of structural variants (SVs) and copy-number variants (CNVs) that are often missed or incorrectly identified using short-read data. Next Level Genomics offers analysis using PacBio SMRT Link and open-source tools, which include Google Deep Variant and other cutting-edge algorithms.
Genome Assembly
Genome Assembly
Long-read sequencing has been proven to be the most useful for the assembly of a de novo genome. Without long-read sequencing, the telomere-to-telomere (T2T) human genome assembly would not have been possible. Long reads allow for regions of the genome not accessible or unable to be assembled to be stitched together and create the lowest number of contigs, the longest contigs, and the most complete genome assemblies. For small genomes like bacteria, plasmids, and viruses, long-read sequencing can often assembly into a whole genome in a in a single contig.
RNA/Iso-Seq Analysis / single-cell RNA
Long-read sequencing is the only method that allows for total analysis of all expressed isoforms of mRNA in a sample. Long reads can often encompass a single mRNA molecule in one read, and analysis often reveals all of the alternative splicing variants from a gene that are otherwise not found with short-read sequencing data. For Oxford Nanopore sequencing, direct, native RNA sequencing is possible; there is no need for cDNA synthesis. For PacBio, the use of the Kinnex concatenation protocol boosts the output of RNA sequencing data by 16-fold. All of this allows for deeper analysis of gene expression and the production of cell typing, clustering, PCA, and other forms of analysis utilizing available tools.
RNA/Iso-Seq Analysis / single-cell RNA
Long-read sequencing is the only method that allows for total analysis of all expressed isoforms of mRNA in a sample. Long reads can often encompass a single mRNA molecule in one read, and analysis often reveals all of the alternative splicing variants from a gene that are otherwise not found with short-read sequencing data. For Oxford Nanopore sequencing, direct, native RNA sequencing is possible; there is no need for cDNA synthesis. For PacBio, the use of the Kinnex concatenation protocol boosts the output of RNA sequencing data by 16-fold. All of this allows for deeper analysis of gene expression and the production of cell typing, clustering, PCA, and other forms of analysis utilizing available tools.
Microbiome / Metagenomics
Whether it’s the full-length 16S rRNA gene in bacteria, the 18S rRNA gene in fungi, or a long-read-based shotgun metagenomic dataset, analysis of the microbiome and metagenomic data from long-read sequencing gives the most comprehensive view of your samples, down to the species and strain level. With the entire rRNA gene sequences, all regions of the gene are included in the data—not just a small amplicon—and classification is more robust and complete with long-read data.
For shotgun metagenomics, assembly of the data from long reads results in many more MAGs (metagenome-assembled genomes) and more complete plasmids and genes within your sample. Next Level Genomics utilizes several commercial and open-source tools for metagenomic analysis for your project and can deliver publication-ready analysis as part of your project.
Spatial Analysis
Next Level Genomics’ spatial services on Nanostring instruments include analysis utilizing on-board software as well as the cloud-based AtoMx system from Nanostring. With AtoMx, your spatial analysis can be performed for normalization, PCA, UMAP, neighborhood analysis, cell segmentation, typing, and much more.
Produce publication-ready images as well as in-depth expression analysis, down to the single cell level.
Microbiome / Metagenomics
Whether it’s the full-length 16S rRNA gene in bacteria, the 18S rRNA gene in fungi, or a long-read-based shotgun metagenomic dataset, analysis of the microbiome and metagenomic data from long-read sequencing gives the most comprehensive view of your samples, down to the species and strain level. With the entire rRNA gene sequences, all regions of the gene are included in the data—not just a small amplicon—and classification is more robust and complete with long-read data.
For shotgun metagenomics, assembly of the data from long reads results in many more MAGs (metagenome-assembled genomes) and more complete plasmids and genes within your sample. Next Level Genomics utilizes several commercial and open-source tools for metagenomic analysis for your project and can deliver publication-ready analysis as part of your project.
Spatial Analysis
Next Level Genomics’ spatial services on Nanostring instruments include analysis utilizing on-board software as well as the cloud-based AtoMx system from Nanostring. With AtoMx, your spatial analysis can be performed for normalization, PCA, UMAP, neighborhood analysis, cell segmentation, typing, and much more.
Produce publication-ready images as well as in-depth expression analysis, down to the single cell level.
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