harvest.readthedocs.io - Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.
Tools
Parsnp - Core-genome...
Genomics is the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as...
Python Programming is a general purpose programming language that is open source, flexible, powerful and easy to use. One of the most important features of python is its rich set of utilities and libraries for data processing and analytics...
bioinformatics.oxfordjournals.org - The genome sequencing revolution is approaching a landmark figure of 1000 completely sequenced genomes. Coupled with fast-declining, per-base sequencing costs, this influx of DNA sequence data has encouraged laboratory scientists to engage large...
genome.edu.au - RNA Seq
Basic Galaxy Tutorial
RNA-Seq tutorial based on Trapnell et al. (2012) Nature Protocols
In this tutorial we cover the concepts of RNA-Seq differential gene expression (DGE) analysis using a very small synthetic dataset from a well...
Integrated solutions CLCbio Genomics Workbench - de novo and reference assembly of Sanger, Roche FLX, Illumina, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection,...
This tutorial is intended to introduce users quickly to the basics of R, focusing on a few common tasks that biologists need to perform some basic analysis: load a table, plot some graphs, and perform some basic statistics. More...