This is a project which is currently making use of HPC facilities at Newcastle University. It is active.
For further information about this project, please contact:
The Bioinformatics Support Unit’s mission is to further biological research through the analysis of data from small experiments to ‘big data’. The unit will utilise the HPC resources provided by comet to fulfil this mission and support omics research projects at Newcastle University. These will primarily focus on two major technologies, firstly transcriptomics, including Single-cell RNA-seq, spatial and bulk tissue analyses and secondly genomics, utilising short-read whole genome and exome sequencing in addition to the analysis of long-read sequencing data.
Transcriptomics:
10X genomics scRNA-seq software: CellRanger and SpaceRanger.
Downstream scRNA-seq: CellBender, Scanpy, Seurat, Muon, EpiTrace, pseudotime.
Bulk RNA-Seq: STAR and Salmon.
Whole genome sequencing:
BWA, GATK, vcftools, multiqc.
Long-read analysis:
EPI2ME, nf-core/scnanoseq.