Welcome to our Galaxy Freiburg newsletter. A lot of new features have been included in the Galaxy framework with the new 16.04 release. Furthermore, we integrated a bunch of new tools and updated the others. Big thanks to the entire Galaxy community which makes this happen! As usual we are happy to take questions on various channels. For more information please read the community section.
- Nested Workflows - Yes Galaxy has now support to include workflows in workflows
- Jupyter Integration: You love IPython? Now you can also use Jupyter with many more Programming Languages like, Ruby, Julia, R, Python2/3 and Haskell
- Interactive Tours are a new way to teach new-comers to analyse their data. Try it out and give us feedback. Go to Help → Interactive Tours and try one of our first tours. We plan to have more in the near future.
- The new data-library should be more stable and way faster than the old one.
- Histories should be able to scale now to many thousands of datasets. We have seen histories with > 100.000 datasts, but we do not recommend it for now ;)
- JBrowse - new Visualisation tool for Genomes, especially good for Genome Annotation
- Prinseq
- RNAcommender
- A bunch of new Kraken tools for metagenomics
- New and faster Text manipulation tools
- Hardklör, Krönik & Morpheus and other Proteomic Tools
- Open Molecule Generator
- AutoDock
- BCF calling tool was added, more to come!
- European Genome-phenome Archive (EGA) integration
- UniProt XML downloader
- Protease Prediction Tool
- A tool for mapping peptides back to genomic locations
- Vegan for our ecologists
- MEME and FIMO
- BAM to SciDX converter
- Trinity
- TransDecoder - identifies candidate coding regions within transcript sequences
- Sickle - A windowed adaptive trimming tool for FASTQ files using quality
- Lighter
- and more ...
Almost all tools :), I will just highlight a few today
- HiSAT
- FASTQC
- TrimGalore!
- TopHat
- BEDtools
- various Exom-Seq tools
- deepTools is now available in version 2
- Next Galaxy workshop is aready scheduled, register here: http://goo.gl/forms/uz9i63FtGc
- The Freiburger Galaxy Team is registered at the Mudiator in Freiburg. Cheer for us - we will need it :)
- The Freiburger Galaxy Team was intervied and a video was published on youtube: https://www.youtube.com/watch?v=t0ebeYV1ZQU
- Galaxy-Tricks: Small but useful tricks you didn't know before
- Many new questions and help in the Q/A forum: https://biostar.usegalaxy.org/
- Use our mailing list to ask questions (galaxy-users@informatik.uni-freiburg.de)
- New Galaxy introduction videos under: https://vimeo.com/galaxyproject
- deepTools version 2
- Debbie has published "DOT1L Activity Promotes Proliferation and Protects Cortical Neural Stem Cells from Activation of ATF4-DDIT3-Mediated ER Stress In Vitro."
- We are annotating tools and services now in Galaxy: "Tools and data services registry: a community effort to document bioinformatics resources."
- Thomas has published "MicroRNA Profiling in Aqueous Humor of Individual Human Eyes by Next-Generation Sequencing."
- Galaxy project: "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update."
For more information have a look at the official newsletters from the Galaxy project
Thanks for reading and happy research!
The Freiburg Galaxy Team