Oxford Nanopore long reads mapped to the reference mitochondrial genomes
High quality DNA was isolated from a pool of adults of S. haematobium (~ 50 pairs) using the Circulomics Tissue Kit (Circulomics, Baltimore, MD). High molecular weight S. haematobium genomic DNA was used to construct two rapid-sequencing (SQK-RAD004; Oxford Nanopore Technologies) and two ligation-sequencing genomic DNA libraries (SQK-LSK109; Oxford Nanopore Technologies), according to the manufacturers instructions. For one rapid-sequencing and one ligation-sequencing library, low molecular weight DNA was removed using the 10 kb-Short Read Eliminator (SRE) kit (Circulomics, Baltimore, MD, USA). Each library was sequenced using separate flow cells (R9.4.1; Oxford Nanopore Technologies). All genomic DNA libraries were sequenced (48 h) on the MinION sequencer (Oxford Nanopore Technologies). Following sequencing, bases were called from raw FAST5 reads using the program Guppy v.3.1.5 (Oxford Nanopore Technologies) and stored in the FASTQ format (Cock et al., 2010).