MitSorter

MitSorter discriminates mitochondrial DNA (mtDNA) reads from nuclear mitochondrial DNA segment (NuMT) reads in Oxford Nanopore Technologies (ONT) sequencing data by exploiting the known lack of CpG methylation in human mtDNA.

Key Features:

• Base modification integration: Incorporates base modification calls directly from raw POD5 files during read alignment.
• BAM partitioning: Produces two separate BAM files from the aligned reads, one containing unmethylated reads and the other containing methylated reads.
• Mutation profile refinement: Enables a more accurate landscape of the mtDNA mutation profile by excluding NuMT contamination.

Scientific Applications:

• Mitochondrial disorder research: Facilitates accurate mapping of the mtDNA mutation spectrum and quantification of heteroplasmy by removing NuMT contamination.
• Genomic research: Applicable to other genomic research areas requiring discrimination of mtDNA from NuMTs in long-read sequencing data.

Methodology:

MitSorter aligns ONT reads to the mitochondrial genome incorporating base modification calls directly from raw POD5 files, then partitions the resulting BAM file into separate BAM files based on methylation status.