Bioinformatics

Contributors: Xinshuai Qi

• HarvardX Biomedical Data Science Open Online Training

  • PH525x series - Biomedical Data Science

  • Bioconductor for Genomic Data Science

• Introduction to Next Generation Sequencing (NGS) Data Analysis - UCI

Genome Assembly

• raw reads clean

• De novo Assembly

  • Trinity

  • Velvet

• Reference-based Assembly

  • Samtools

  • VCFtools

  • BCFtools

Genome Evolution and Genomics

• OrthoFinder

• Circos

• SnpEff

• Gene Ontology

• LeafJ

Phylogenetics

• RAxML

• PAML

• BEAST

• TreeMix

Population Genetics and phylogeography

• STRUCTURE

• PCA and smartPCA

• Provean

• BadMutation

• HAPMIX

• ∂a∂i

• DIY-ABC

• fastSimCoal

• SLiM2

• TCS

• Ecological Niche Modeling

  • WorldClim

RNASeq

• TopHat

• WGCNA

• Cufflinks

Quantitative Genetics and GWAS

• PLink

• R/qtl

Long-read sequencing (PacBio and MinION)