Expertise

We implemented a routine cost-effective single-cell sequencing service for 10x Genomics libraries and other single cell libraries using our Illumina NovaSeq6000 platform (shallow-seq and deep sequencing), and also offer data-analysis support. This is part of a complete one-stop solution for single-cell analysis with the VIB Single Cell core facility

VIB Nucleomics Core has a routine pipeline developed for cost-effective mRNA-seq using single-end 100 cycles reads for differential gene expression purpose. Besides that, it also offers sequencing and downstream analysis for total RNA-seq (incuding lncRNAs), mRNA-seq (analysis of splice-variants) and smallRNA-seq. Using our PacBio Revio, full-length transcript isoform cataloging is also possible in order to support novel genome annotation projects (IsoSeq).

For genomic analysis, we offer whole genome sequencing using our Illumina NGS portfolio or using Pacbio HiFi long-reads on the Revio system (identifies structural variants in addition to short variants and provides DNA methylation data). De-novo genome assembly for organisms smaller than few 100 MB (including microorganisms) can also be done using Pacbio HiFi long-reads on the Revio system. De-novo assembly of larger genomes on ONT Promethion should be discussed with our colleagues from VIB GSF (Antwerp).

Whole exome sequencing (WES) is a sequencing approach targeting the protein-coding regions of all genes (known as the exome). The exome makes up around 1% of a genome and allow the sequencing of multiple samples in a run as it needs less sequencing depth than whole genome sequencing applications. On the other side, this approach is limited to the well-annotated genomes such as mouse and human. To perform WES, VIB Nucleomics Core uses the Element Trinity workflow with Twist Exome 2.0 panel and the sequenicng is done on Element Bio AVITI sequencing platform.

We have a full-length 16S rRNA profiling (V1-V9) service running on the Pacbio Revio platform. We also integrated a cost-effective solution for shotgun metagenomic analysis by making use of our Short Read sequencing platforms.

See our full application note about the performance data, depth guidelines, and the complete bioinformatics workflow.

Paired-end sequencing on our short reads sequencing platforms are used for targeted sequencing applications. We can use custom or panel sequencing assays. Amplicon sequencing using PacBio HiFi long-read sequencing can be used to sequence amplicons up to 10kb including full length V1V9 16S rDNA or ITS amplicons.

VIB Nucleomics Core offers solutions to map and quantify genomes and transcriptomes that explain phenotypes of interest. With bioinformatics support as an integral part of our service, the solutions truly range from sample to science.
You are not left behind with raw data files after lab experimentation. Our bioinformatics team can guide you through the complex data analysis process and connect you back to your original research question with new scientific insights. Besides regular data quality assessment, data preprocessing, and mapping, our team has many years of experience in comparative analysis, functional analysis, predictive modeling, and assembly & NGS scaffolding for genome finishing purposes.