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The latest releases, updates, and bugfixes in KBase 🛠️
Dec 17, 2025

App Releases and Updates Q4 2025

New App: Assess Reads Quality with NanoPlot

Check out our new app for quality assessment of long reads sequencing data: Assess Reads Quality with NanoPlot. NanoPlot produces several plots with information about read quality, length distributions, N50, and cumulative yield for quality assessment and control of read libraries in a convenient HTML report.

Update: Classify Taxonomy of Metagenomic Reads with Kaiju

The popular taxonomy app Classify Taxonomy of Metagenomic Reads with Kaiju was upgraded to use the latest reference databases available for classification. Users should note that these newer databases will result in different classifications for their reads, with changes in the underlying data and taxonomic nomenclature. As the original Kaiju webserver is no longer available as of 2024, KBase remains a reliable platform for this reads-based taxonomy tool. 

Bugfix: Classify Microbes with GTDB-Tk

The user science support team diagnosed and fixed a highly reported bug in the Classify Microbes with GTDB-Tk app that produced a “list index out of range” error code. We encourage any users who have experienced this bug to re-run GTDB to check that it has been resolved. As always, please report any errors with KBase apps to our Help Board.

About the Authors

Ben Allen
Ben Allen
Zach Crockett
Zach Crockett
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.

Zach Crockett
Zach Crockett

Zach Crockett is a member of the outreach, communications, and user development team. His background is in biochemistry and cellular biology. He has professional experience in medical lab science testing information management systems, creating training plans, improving processes, and developing standard operating procedures.

DOE Systems Biology Knowledgebase
DOEKBase
engage@kbase.us
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