Jun 12, 2023

App Releases and Updates Q2 2023

New Report Viewer Apps

series of new apps have been released that enable users to produce downloadable text files for most types data objects in KBase. Use these apps to create files for your KBase data that you can use with local tools such as Excel or bioinformatics scripts. These “Object Info” apps are available for Assemblies, Assembly Sets, Genomes, Genome Sets, Genome Comparisons, Feature Sets, Domain Annotations, Multiple Sequence Alignments, and Proteome Comparisons. Load these apps into your Narrative from the Utilities category in the Apps panel.

Kaiju Version and Databases Upgrades

Classify Taxonomy of Metagenomic Reads with Kaiju has been updated to version 1.9.0 and its reference classification databases upgraded to those released in 2022. The latest version deployed in KBase defaults to using a higher sensitivity and more memory intensive taxonomy classification algorithm and optimizes the summary table of taxon abundances. The reference database upgrades add taxonomic classification for fungi and viruses, alongside improvements to bacterial and archaeal taxa. 

FastQC Updated to Version 12.1

Assess Read Quality with FastQC has been updated to the latest public release. Version 12.1 adds functionality like SVG export for figures and adds polyA/G sequences to the Adapter Content visualization. Learn about additional bug fixes and improvements in the release notes. 

About the Authors

Ben Allen
Ben Allen

Ben Allen coordinates outreach and user development activities to build the KBase user community while engaging in scientific collaborations to advance the use of the platform. His background in biochemistry and science education helps him develop protocols and training materials that provide depth while being accessible to a wide audience. Research interests include systems biology, microbial ecology, bioremediation studies, and biology education.