# Bioinformatics

* [HarvardX Biomedical Data Science Open Online Training](http://rafalab.github.io/pages/harvardx.html)
  * [PH525x series - Biomedical Data Science](http://genomicsclass.github.io/book/)
  * [Bioconductor for Genomic Data Science](http://kasperdanielhansen.github.io/genbioconductor/)
* [Introduction to Next Generation Sequencing (NGS) Data Analysis - UCI](https://www.google.com/url?sa=t\&rct=j\&q=\&esrc=s\&source=web\&cd=1\&cad=rja\&uact=8\&ved=0ahUKEwjJ7fDmk8vWAhVY4WMKHZLACpIQFggqMAA\&url=http%3A%2F%2Fcbt.bio.uci.edu%2Ffiles%2F2016%2F01%2FPresentation-2-jwu_4Jan16.pdf\&usg=AFQjCNE7T56mHrL5Lyt3ttpEdDVkrI_Efg)

### 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](https://nanoporetech.com/products/minion))