Project Contacts

For further information about this project, please contact:

• Dr James Stewart (jim.stewart@newcastle.ac.uk)
• Dr Thomas Nicholls (thomas.nicholls@newcastle.ac.uk)

Project Description

The project uses either sort-read (Illumina) or long-read (Oxford Nanopore) to detect structuraal rearrangment or insertion/deletion mutations in the mitochondrial DNA from cells or tissue samples

Software or Compute Methods

For our long read sequencing project to investigate mtDNA replication we use a pipeline that features Dorado software from. Oxford Nanopore, to basecall, demultiplex and align or sequencing runs and DNAscent2 to call thymidine analogues incorporated during mtDNA replication. In addition, we use SAMtools and BEDtools for further downstream analysis. DNAscent2 link: https://www.nature.com/articles/s41467-025-63168-w



To call deletions in short read sequencing we utilise HIsat2 as well as BOWtie2 for the alignment together with SAMtools and BEDTools for downstream analysis and MitoSALT for the identification of breakpoints in mtDNA. This part of the work also uses variant callers such as Sniffles to detect variants in the alignments. MitoSALT link: https://pmc.ncbi.nlm.nih.gov/articles/PMC7769605/