Parasite Genomics: Methods and Protocols

Part I: Novel Sequencing and Bioinformatic Pipelines for the Study of Parasite Genomes

1. Nanopore Long Read DNA Sequencing of Protozoan Parasites: Hybrid Genome Assembly of Trypanosoma cruzi

Florencia D燰z-Viraqu? Gonzalo Greif, Luisa Bern? and Carlos Robello

2. Chromosomes Conformation Capture Coupled with Next Generation Sequencing (Hi-C) in Plasmodium falciparum

Mohit Gupta, Todd Lenz, and Karine G. Le Roch

3. Sequencing and Reconstructing Helminth Mitochondrial Fenomes Directly from Genomic Next-Generation Sequencing Data

Nikola Palevich and Paul Haydon Maclean

4. Automated Phylogenetic Analysis Using Best Reciprocal BLAST

Erin R. Butterfield, James C. Abbott, and Mark C. Field

Part II: Diagnostic Approaches Using Genomic Tools

5. An Illumina MiSeq-Based Amplicon Sequencing Method for the Detection of Mixed Parasite Infections Using the Blastocystis SSU rRNA Gene as an Example

Jenny G. Maloney, Nadja S. George, Aleksey Molokin, and Monica Santin

6. Giardia duodenalis: Detection by Quantitative Real-Time PCR and Molecular Diversity

Alejandro Dashti, Pamela C. K飉ter, and David Carmena

Part III: Host-Parasite Interactions: Deciphering Gene Function and Molecular Processes in Parasites

7. Conditional Gene Deletion in Mammalian and Mosquito Stages of Plasmodium berghei Using Dimerizable Cre Recombinase

Priyanka Fernandes, Manon Loubens, Olivier Silvie, and Sylvie Briquet

8. Coupling Auxin-Inducible Degron System with Ultrastructure Expansion Microscopy to Accelerate the Discovery of Gene Function in Toxoplasma gondii

9. Genome-Wide Analysis of RNA-Protein Interactions in Plasmodium falciparum Using eCLIP-Seq

Thomas Hollin, Steven Abel, and Karine G. Le Roch

10. Transcriptional Analysis of Tightly Synchronized Plasmodium falciparum Intraerythrocytic Stages by RT-qPCR

Nia Casas-Vila, Anastasia K. Pickford, Harvie P. Portugaliza, Elisabet Tint?Font, and Alfred Cort廥

11. Analysis of the Interaction between Plasmodium falciparum-Infected Erythrocytes and Human Endothelial Cells Using a Laminar Flow System, Bioinformatic Tracking and Transcriptome Analysis

Yifan Wu, Philip Bouws, Stephan Lorenzen, Iris Bruchhaus, and Nahla Galal Metwally

12. Integration of Genomic and Transcriptomic Data to Elucidate Molecular Processes in Babesia divergens

Luis Miguel Gonz嫮ez, Elena Sevilla, Miguel Fern嫕dez-Garc燰, Alejandro S嫕chez-Flores, and Estrella Montero

13. Integration of Functional Genomic, T