Websites

Galaxy: Galaxy is an open source, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. Galaxy project,  Galaxy wiki, Galaxy/Rätsch Lab, Galaxy/qbrc

GenomeSpace: GenomeSpace is a cloud-based interoperability framework to support integrative genomics analysis through an easy-to-use Web interface. GenomeSpace provides access to a diverse range of bioinformatics tools, and bridges the gaps between the tools, making it easy to leverage the available analyses and visualizations in each of them. The tools retain their native look and feel, with GenomeSpace providing frictionless conduits between them through a lightweight interoperability layer. More info can be found from the related paper: Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace 

NGS WikiBook:  a dynamic collaborative online training effort with long-term sustainability for next-generation sequencing (NGS) analysis. Nine rules to begin with NGS analysis: **1) Do not fear the command line; 2) Known the conventions; 3)Read introductory reviews; 4) Start with quality checking; 5) Plan for mistakes and document workflow; 6) Always get informed and get help if stuck; 7) Use an efficient integrative approach; 8) Avoid reinventing the wheel; 9) Education is important. **

NGS Software list: a regularly updated list of NGS software collected by http://seqanswers.com/wiki.

Wardrobe:  BioWardrobe Experiment Management System, which allows users to store, visualize and analyze epigenomic and transcriptomic next-generation sequencing data using a biologist-friendly, web-based graphical user interface without the need for programming expertize.