Appendix: List of Tools used

Basecalling

• Guppy (available at Oxford Nanopore Community)

Quality Control

• FastQC
• PycoQC
• MinION_QC

Read filtering & trimming

• Porechop
• Nanofilt

Assemblers

• Miniasm
• Flye
• Shasta

Read Mappers

• Minimap2
• BWA

Assembly assessment & visualisation

• Assemblytics
• Mummer
• Bandage
• IGV

Error correction

• Racon
• Minipolish
• Medaka
• Pilon

Variant Calling

• Sniffles

Others

• Samtools