Portable and cost-effective genetic detection and characterization of Plasmodium falciparum hrp2 using the MinION sequencer

This repository contains scripts, Jupyter notebooks, and visualizations supporting the manuscript "Portable and cost-effective genetic detection and characterization of Plasmodium falciparum hrp2 using the MinION sequencer" (under revision).

The analysis folder contains scripts and Jupyter notebooks used to analyze MinION sequencing data following basecalling and barcoding with MinKnow (Oxford Nanopore Technologies), as performed during sequencing.

• alignment with minimap2
• alignment cleanup and assessment with samtools and Qualimap
• de novo assembly with canu
• figure generation and coverage threshold calculations with python
• repeat-typing with python

Workflow diagram