Bioinformatics
Our bioinformatics team supports both short- and long-read sequencing projects, from planning experiments to analysing and interpreting sequencing data. We help researchers define appropriate experimental and sequencing strategies, select workflows suited to their biological questions, and make sense of the resulting data.
Our core offerings include:
Long-read bioinformatics
Basecalling, Quality control and Demultiplexing: Processing of sequencing data and assessment of sequencing data quality.
Methylation calling: Analysis support for identifying DNA and RNA methylation patterns.
Alignment: Mapping long reads to a reference genome or transcriptome.
Assembly: Initial de novo assembly of small genomes and generation of read contigs.
Variant calling: Detection of sequence variants (SNVs, SVs) from long-read data, including setup and per-sample analysis.
Iso-Seq / isoform analysis: Analysis of full-length transcript sequencing data, including isoform identification and characterisation.
Short-read bioinformatics
Quality control and demultiplexing: Processing of sequencing data and assessment of library and read quality.
Single-cell and 10x Genomics analysis: Analysis workflows for single-cell RNA-seq and related 10x Genomics datasets. 16S amplicon analysis: Analysis of Illumina 16S V3–V4 and V4 sequencing projects.
Alignment: Reference-based alignment for RNA-seq, ChIP-seq, ATAC-seq, miRNA-seq, and 10x Genomics data. Differential gene-expression analysis: Statistical comparison of gene expression between experimental conditions. ATAC-seq and ChIP-seq analysis: Peak calling and differential chromatin-accessibility analysis.
Variant calling: SNP alignment, calling, and differential SNP analysis.
Transcript assembly and annotation: De novo or genome-guided transcript assembly and annotation.
Methylation Analysis: Identification and quantification of DNA methylation patterns from suitable sequencing data and identification of differentially methylated regions or sites between experimental conditions.
Hi-C Analysis: Generation of genome-wide chromatin contact maps from suitable sequencing data following reference-based alignment.Identification and characterization of topologically associating domains (TADs) and chromatin loops from contact maps.
Custom projects and project planning
For projects that require more than our standard analysis workflows, we provide tailored bioinformatics support at every stage. This includes planning experiments and sequencing strategies before data generation, as well as developing and carrying out customised analyses once data are available. Depending on the project, we can advise on data requirements, workflow selection, and approaches for interpreting the results.