- New Tool: Collapse Collection converts to single datasets January 8, 2021 - Data stuck in a dataset collection or list when you need it as a single dataset? When you have a history entry in a ‘Collection’, those files can be extracted as single history entries using the Collapse Collections into a single dataset tool. Galaxy was developed as a platform to handle large datasets. The abilityLearn More...
- Tool panel reorganization December 10, 2020 - Does something look different around here? The tool list has been completely reorganized! There are new section headers and groupings to aid in navigating to the exact tool you need, as well as discovering tools you may not have known we have, so do some exploring! Additionally, you will notice a section called ‘Commonly UsedLearn More...
- New Tool: Compare Genbanks December 9, 2020 - Genome annotations are constantly improving. In the process of working on an annotation, or re-annotation, project, you can accumulate various Genbank file versions for the same organism. When you need a wholesale comparison of the number, position/length, and names or notes for each CDS feature, try using our new Compare Genbanks tool. The tool willLearn More...
- Tip: how to extract an SVG file for figure generation December 8, 2020 - Want to publish your Galaxy analyses outputs but hampered by the inability to download high-resolution, editable files of the results for your next manuscript figures? Sometimes we are too and that is what prompted the creation of our latest training material entry under the Additional Analyses section called “How to Extract an SVG file fromLearn More...
- Training materials on workflow use added December 7, 2020 - Need an introduction to using workflows? Our newest training material entry under Introduction to Galaxy and Apollo is called “Using and Editing Workflows in Galaxy“. This quick guide covers the basics of accessing, running, and creating workflows to automatically chain Galaxy tools together for reproducible job execution with minimal clicks. The material may also beLearn More...
- New Tool: MultiQC November 30, 2020 - We have integrated a handy tool from https://multiqc.info/ into CPT Galaxy that allows aggregation of bioinformatic analyses into an HTML report output. The MultiQC tool is particularly useful in conjunction with FastQC when used on NGS data. Added by Cory Maughmer, the MultiQC tool can be found under CPT: Genomic Overview. Please email the supportLearn More...
- Tool Spotlight: MIST dot plots November 27, 2020 - Do you want to compare a large number of phage genomes by dot plot? In the Comparative Genomics workflow, we regularly do genome-wide nucleotide comparisons between 5-10 or more genomes. The dot plot generated by MIST is a primary output from that analysis. Some improvements to labeling placement have been made to optimize readability whenLearn More...
- Tool spotlight: Interrupted gene detection tool November 26, 2020 - The Interrupted genes detection tool, widely used as part of the Functional Annotation Workflow has been renamed (formerly called the Intron Detection tool) to reflect the broader applications for which it can be used. Though originally written to parse protein BLAST results and identify genes possibly interrupted by introns, repeated use demonstrated that this toolLearn More...
- Tutorial materials updated November 25, 2020 - Noticed any changes around here recently? In the past few months, we have performed significant maintenance on the entire CPT Galaxy and Apollo ecosystems. In addition to updating the platforms to current community releases, many workflows and tools were modified to improve functionality and efficiency. To keep both seasoned and new users up to speedLearn More...
- New Tool: Deduplicate FastQ files November 11, 2020 - Tired of waiting so long for an assembly? Maybe the Deduplicate FastQ tool is for you. It will quickly and efficiently reduce your FastQ datasets to only unique entries. The reduced dataset will have faster downstream processing. This external tool added by Anthony Criscione can be found under CPT: OTHER. Please email the support teamLearn More...