Metagenomic sequencing of CSF samples

Project title
Metagenomic sequencing of CSF samples.

People involved
Principal investigators: Nicola Mulder
Co-investigators: Adrian Brink and Diana Hardie
Support request made by: Gert Marais
Bioinformatics support team: Ephifania Geza and Gerrit Botha

Short description of project
Given 47 patients (each sequencing run includes 10 patients and 2 controls on an Illumina MiSeq platform running 600 cycle v3 kits generating ±(10-15) Gb of short read data per run), this project is aimed at developing a bioinformatics pipeline that facilitates the prediction of the patient's disease phenotype based on polymorphisms in loci relevant to infectious responses.

Objectives

1. To perform nucleotide metagenomics
2. Protein similarity and
3. Transcriptome analysis