Fig. 2: Flowchart detailing informatics analysis pipeline steps for Cas9-mtDNA-enrichment sequencing.
From: A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome
After sequencing and basecalling, FASTQ reads are mapped against the reference GRCh38. Afterwards the reads are filtered and demultiplexed. The second mapping against a custom reference is critical for avoiding split reads. Then the baldur software does the variant calling for each demultiplexed sample. Resulting VCFs are used for downstream analysis for the annotation of the variants. Created in Lucidchart (www.lucidchart.com).
