NGI during Covid-19 outbreak

NGI is still up and running during the Covid-19 pandemic, but we are experiencing some limitations in terms of personnel and key reagents. Each NGI node is following its respective host university recommendations and will continue operation until further notice.

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PacBio SMRT sequencing

PacBio SMRT sequencing generates reads tens of kilobases in length enabling high quality genome assembly, structural variant analysis, amplicon resequencing, full-length transcript isoform sequencing, full-length 16S rRNA sequencing and amplification free epigenetic characterization.

PacBio Sequel utilizes the Single Molecule Real Time Sequencing (SMRT) technology which provides high sensitivity, high throughput and fast turnaround times. It is suitable for all types of de novo genome sequencing, analysis of structural variation and full-length transcript isoform sequencing. Other typical applications include meta-barcode studies and pooled amplicons, as sequencing bias toward shorter fragments is low. Since no amplification is required prior to sequencing, methylations in genomic DNA can be detected by analysing interpulse duration times.


DNA sequencing

With the capacity to generate long reads of very high accuracy it is suitable for all types of de novo genome sequencing, analysis of structural variation and amplicon-based sequencing.

de novo assembly

PacBio de novo genome assemblies deliver megabase-size contig N50s, consensus accuracies >99.99%, and phased haplotypes so you can generate reference-quality assemblies of diverse species and populations. Whole genome sequencing for de novo assembly enables to characterize the complete genetic diversity within a species, to develop population-specific reference genomes to drive precision medicine and assemble microbial genomes and their plasmids in a single experiment. We have experience sequencing a vast range of organisms and genome sizes and can help with everything from DNA extraction to genome assembly.

Genome resequencing

PacBio can be used for whole genome resequencing for phasing and variant detection. The long sequence reads enable characterization of complex structural variants also in complex regions of the genome.

Targeted resequencing (amplicon sequencing)

Amplicon sequencing involves sequencing of PCR-amplified loci across large sets of samples. PacBio can be used to generate highly accurate sequences from amplicons ranging in size from several hundred bases to 10 kb or larger.

Environmental sequencing

PacBio sequencing allows for the identification of individual members of complex microbial populations, with 16S rRNA species-level identification and complete plasmids or viral quasispecies. This technology can resolve complex populations in viral or metagenomic samples, map order and orientation of multiple-inserted phage element, facilitate study of viral integration and integration sites, perform multiplexed multi-locus sequence typing (MLST).


RNA sequencing

Single Molecule, Real-Time (SMRT) Sequencing and Iso-Seq analysis allow you to generate full-length cDNA sequences, with no assembly required. This makes it an ideal method to characterize transcript isoforms within targeted genes or across an entire transcriptome. PacBio Iso-Seq analysis enables discovery of new genes, transcripts and alternative splicing events. It will help improve genome annotation to identify gene structure, regulatory elements and coding regions. The iso-form level resolution may also be used to increase accuracy of RNA-seq quantification generated from short-read data.

Read more about RNA sequencing: Human applications or Plants and animals.


Epigenetics

Single Molecule, Real-Time (SMRT) Sequencing is amplification free and can therefore directly detect epigenetic modifications by measuring kinetic variation during base incorporation. Modification data is captured simultaneously with sequence data, thus eliminating the need for special sample preparation and additional sequencing. Deep coverage is required to resolve the modification signals and it is therefore primarily recommended for microbial genomes. The m6A and m4C methylation status can be determined at each position using this method.

Read more about PacBio epigenetic application here.


User-prepared libraries

NGI accepts user-prepared libraries for PacBio sequencing on both the Sequel and Sequel II instruments. Please contact a project coordinator for further information.

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Service

We are routinely running this method. Please visit the Order Portal to place an order.

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