Table of Contents

Genomics

Genomics is an interdisciplinary field of molecular biology concerning function, structure, organisation, evolution and editing of genomes. The past two decades have led to the development of a plethora of sequencing methods, which address different aspects within the field of genomics. We offer analyses for a variety of genomic sequencing applications:

Genome Annotation

Genome annotation is the process of identifying structural features in genomes and determining their function. Learning how genomes are organised is immensely valuable for gaining a better understanding of organisms and their evolution.

We provide a computational approach to genome annotation. Here, we incorporate multiple types of evidence for both structural and functional annotation of any organism with a completed reference genome. Evidence sources include short- and long-read RNA sequencing data, proteomics data and ab initio gene predictions. By leveraging multiple evidence types at once, we are able to rapidly deliver genome annotations and output them in most popular formats such as GTF or GFF.

Variant Interpretation

Variant calling and interpretation is the process of identifying and annotating genetic variants from sequencing data. Investigating the functional impact of such variants has transformed the understanding of human health and disease.

We help identify and interpret genetic variants in any type of setting. To achieve this, we continuously evaluate new variant callers and interpretation technologies as they are released. This enables us to stay up-to-date with the latest methodologies while delivering results with industry-grade precision and recall.

Methylation Calling

Methylation calling is the process of identifying patterns of DNA methylation from bisulfite sequencing (Bis-Seq) experiments at a genome-wide scale. Studying DNA methylation is important for gaining a better understanding of how epigenetic markers impact gene expression and organism development.

We offer analysis of whole-genome bisulfite sequencing data for genome-wide identification of cytosine methylation at single-nucleotide resolution. This is achieved using an up-to-date toolchain, ensuring reliable results. We also perform downstream analyses such as methylome vs gene expression correlations, in the cases where gene expression data is available.

ChIP-Seq Analysis

Chromatin immunoprecipitation sequencing (ChIP-Seq) is used for identifying genomic binding sites of DNA binding proteins. Exploring global DNA-protein interactions is crucial for expanding our knowledge of how transcription factors (and any other type of chromatin-associated proteins) may influence fundamental biological processes such as gene expression.

We provide analysis of ChIP-Seq data for genome-wide identification of immunoprecipitated protein factor binding sites. This is achieved using a state-of-the-art toolchain that only incorporates peak calling algorithms which consistently score high in comparative studies. We also perform downstream analyses of identified peaks such as chromatin state annotations (genomic region classification upon typical epigenomic patternsĀ  for promoters, enhancers, transcribed or repressed regions).

ATAC-Seq Analysis

Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq) is used for assessing genome-wide chromatin accessibility. Investigating chromatin accessibility is fundamental for understanding how the packing and structural organisation of chromatin in cellular nuclei affects the development of both specific phenotypes.

We offer analysis of ATAC-Seq data for genome-wide identification of accessible regions. This is achieved using a toolchain that has been fully optimised for ATAC-Seq peak calling, incorporating calling algorithms that consistently score high in comparative studies. We also perform a range of downstream analysis such as differential peak analysis and nucleosome positioning.

Want to discuss a genomics project?

We are always eager to learn about exciting new research, please get in touch!