Nextflow pipeline for plasmodium SNP calling

Pangenome-Analysis.py is written for extraction of core, accessory and unique genomes (Gene families and proteins) along with filtration of single copy orthologues, creation of binary and count matrices as well as removal of duplicates.

Creates a construct developed by the Niles Lab at MIT, designed to deliver a 3' UTR post-transcriptional regulatory element payload to a specific given gene in Plasmodium falciparum.

Illustrative analysis showing how population genetic structure discovery in Plasmodium genetic data using principal coordinates analysis and hierarchical clustering is sensitive to the pairwise genetic distance and the clustering linkage function

Plasmodium berghei sporozoites were dissected from An. stephensi mosquitoes and isolated into microdroplets to generate single-cell RNA libraries. After sequencing, reads were aligned to the Pb genome, and analysed using various single-cell tools.

My work during internship in Walter+Eliza Hall Institute of Medical Research

This repository contains data and code for our analysis of the genome of a Plasmodium falciparum strain with reduced susceptibility to Artemisinin-Based Combination Therapy (ACT) drugs. We performed whole-genome sequencing of the HSOG3 clinical isolate and compared it with a large dataset of global P. falciparum samples.

Calculating the coverage depth for each coding gene and the percentage of each gene covered at ≥ 10X depth.