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 on NovaSeq6000 (SE100bp reads) for differential gene expression purpose. Besides that, it also offers Illumina sequencing and downstream analysis for total RNA-seq (incuding lncRNAs), mRNA-seq (analysis of splice-variants), and smallRNA-seq. Some smaller depth applications can use the cheaper ONT Flongle devices. Full length mRNA sequencing is offered on our GridION platform, while full-length cDNA sequencing can be done using GridION or Sequel. 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 and capture-based sequencing (exome, ChIP-seq, targeted resequencing, CRISPR/Cas libraries) using our Illumina NGS portfolio. De-novo genome assembly for organisms smaller than few 100 MB is done using our long-read instrument portfolio. De-novo assembly of larger genomes on ONT Promethion is offered through collaboration with our colleagues from VIB GSF (Antwerp).  Cost-effective de-novo assembly of microorganisms is feasible using ONT’s flongle solution. We also offer native DNA modification sequencing (mainly bacteria) through our long-read instrument portfolio.

We have a full-length 16S rRNA profiling (V1-V9) service running on the Sequel IIe platform. Metagenomics analysis of full-length rRNA operons occurs using UMI long-read and nanopore amplicon-sequencing (ONT). We also integrated a cost-effective solution for shotgun metagenomic analysis by making use of our Short Read sequencing platforms.

Illumina MiSeq and NovaSeq (paired-end 250bp sequencing) are used for targeted sequencing applications: custom sequencing assays, targeted resequencing, and metagenomic 16S rRNA profiling. Long-read sequencing can be used to perform amplicon sequencing in order to identify new splice variants or gene fusions.

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.