Docker – This is not specific for bioinformatics, but I’ve put together a Dockerfile that contains a large suite of bioinformatics software that you can use to create your own container (i.e. a virtual Linux computer that will run all of the software contained in the Dockerfile).
Cyverse (formerly iPlant Collaborative) – Web-based bioinformatcs suite. Nearly every bioinformatic tool you could think of and it’s SUPER fast! Plus, unlimited file storage (both size & duration) and custom app development! Our current go-to tool.
SQLShare – Developed by University of Washington’s own eScience Institute, this is a web-based tool to simplify the use of SQL databases for large dataset manipulation for non-computer people. This tool has become indispensable for manipulating extremely large datasets in a timely fashion for us.
Galaxy – Web-based bioinformatics suite, similar to iPlant, but with a slightly better user interface. However, due to file quotas and it’s slow response time (both in data uploading and manipulation), we have mostly stopped using it.
Integrative Genomics Viewer (IGV) – Software for aligning and visualizing annotated genomic sequences. Comes with a long list of available genomes, but allows utilization of custom genomes. Software is Java-based and requires download/installation.