ONT sequencing of Glossina fuscipes from a wild Uganda population: adult female whole insect
HMW DNA was extracted with the NEB Monarch Genomic DNA Purification Kit (NEB, MA, USA), following the manufacturer's suggested modifications for insects. Additionally, short reads were depleted using the SRE XS kit (PacBio, CA, USA). An ONT LSK14 ligation library was prepared, following standard protocols except for increasing input HMW DNA to between 2000 ng and 3000 ng to produce a more concentrated library. The library was sequenced on a ONT 10.4.1 minION flow cell for 48 hours. Sequencing throughput was increased by stopping the sequencing run every 12 to 16 hours to wash the flow cells with the ONT wash kit v4 and to reload fresh library. Generated POD5 signal data files were basecalled and adapter trimmed with Dorado v0.9.1 using the simplex SUP basecalling model. Produced BAM files were converted to FASTQ files with Samtools and filtered with nanoq v0.10 to q10 and minimum 500 bp read length.