Home - BGIGPD/BestPractices4Pathogenomics GitHub Wiki
Welcome to the BestPractices4Pathogenomics wiki!
Course content
- Day 01 - Introduction
Chapter 1: Basic knowledge
- Day 02 - Bioinformatics methodology
- Day 03 - Data Manipulation and visualization
- Day 04 - Quality control: Case from publications
- Day 05 - Bioinformatics skills: Basic Linux commands
- Day 06 - Quality Manipulation: SeqKit for sequence data
- Day 06 - Quality Manipulation: SeqKit tasks for virus
- Day 07 - Quality control: Read quality control and read assembly
- Day 08 - Quality control: Reads host removal and rRNA removal
- Day 09 - Bioinformatics skills: R Basic Commands
- Day 10 - Quality control: Assembly quality assessment
Chapter 2: Virome analysis
- Day 11 - Virus Identification & Viral genome quality assessment
- Day 12 - Consensus Sequence Generation for Virus Genome using Alignment-based Methods
- Day 13 - Homologous Virus Sequence Search and Multiple Sequence Alignment
- Day 14 - Construction of evolutionary tree
- Day 15 - Virus recombination
- Day 16 - Part 1. Virus genes annotation | Part 2. Virus diversity
Chapter 3:Parasite and mosquito population analysis
- Day 18 - Part 1. VCF annotation | Part 2. VCF Manipulation & Filtering | Part 3. SNP Phylogeny Construction
- Day 19 - Population structure (PCA, admixture, Fst)
- Day 20 - Population visualization in R
- Day 21 - Detection of insecticide‐resistant genes in mosquitoes and malaria