The Broad Institute

• Genome Analysis Toolkit
• Integrative Genomics Viewer

Cytoscape Tutorials https://github.com/cytoscape/cytoscape-tutorials/wiki

EMBL-EBI  http://www.ebi.ac.uk/
The European Molecular Biology Laborator-European Bioinformatics Institute has many tools that address the entire range of bioinformatics analyses from genes and genomics, gene expression, pathways, proteins and proteomics and small molecules. The training pages have links to workshops as well as on-line training. Training tutorials and video workshops can be filtered by topic, level and duration.

Ensembl:  www.ensembl.org/

• The Ensembl Project, a joint effort the EMBL-EBI and Sanger Centre, does automatic annotation of genomes and integrates other data (phenotype, variation, regulation) and provides a browser to view that data in the context of the genome. Ensembl has genomes for many organisms and powerful tools for viewing data (including your own) and mining and downloading data.

• Tutorials on using the Ensembl Genome Browser, finding and downloading data, and uploading and viewing data
  http://www.ensembl.org/info/website/tutorials/index.html.                

NCBI Educational Page: http://www.ncbi.nlm.nih.gov/education/
The National Center for Biotechnology Information is a major source of gene-based information including genome and gene sequence, variation and function, and protein sequence, structure and function, as well as PubMed. The Education Page can help you to use these databases and tools effectively.

• Getting Started: How-to Guides  http://www.ncbi.nlm.nih.gov/guide/all/#howtos  for directions on using NCBI tools to answer questions such as finding the function of a gene, finding human variation associated with a phenotype or disease, or viewing the SNPs of a gene.

• Teaching Resources: Tutorials  http://www.ncbi.nlm.nih.gov/education/tutorials/  for Web Tutorials for BLAST, 3D Structures and Modeling, and viewing using Cn3D

• Documentation: Fact Sheets and Instructions:  http://www.ncbi.nlm.nih.gov/education/factsheets/ describe how to use various tools using screenshot-based instructions.

• NCBI Videos on YouTube  http://www.youtube.com/NCBINLM
  for tutorials on using NCBI resources, Gene Expression, Analyzing data, using Genome Workbench, NCBI's tool for viewing and analyzing sequence data.

UCSC Genome Browser: http://genome.ucsc.edu/
UCSC provides access to annotations of epigenetic regulation from ENCODE, the Encyclopedia of DNA Elements that influence gene expression. The UCSC Genome Browser allows one to view the genome with tracks showing expression of these elements, such as histone modification, DNA methylation, and DNAse hypersensitivity, in a variety of different tissues. By zooming the view down the elements can be viewed at the sequence level.

• The sequence of the Neandertal genome is available and can be viewed in comparison to the human genome.
• The UCSC Genome Browser Help tab has information on how to use the browser. Additional training and help can be found at
  https://genome.ucsc.edu/training.html

Video Tutorials from NH-INBRE: http://nhinbre.org/bioinformatics-modules/

Introduction to Applied Bioinformatics: http://readiab.org/ (from the Daporaso Laboratory)