Learn how KBase can help you

Learn how KBase can help you

Explore tutorials, documentation, and FAQs about the KBase platform.

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Analysis Apps in KBase

Analysis Apps in KBase

KBase Apps are analysis tools that you can use in KBase. Apps interoperate seamlessly to enable a range of scientific workflows (see figure below). Some of the apps were written by KBase scientists and developers; others are third-party tools that were integrated into KBase with our Software Developer Kit (SDK). The number of apps available in KBase increases as members of the community use our SDK to integrate their analysis tools into the KBase platform.

The App Catalog lists all of the currently available apps. The majority of them fall into the following categories:

Assembly and Annotation

KBase provides multiple Apps for de novo assembly of Next-Generation Sequencing (NGS) reads from various sequencing platforms. These assemblies can be annotated with RAST or Prokka, enabling you to explore structural and functional features.

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Sequence Analysis

KBase has a suite of Apps to perform various sequence analyses. They provide the ability to assess quality, search for matches within local databases, and perform multiple sequence alignments.

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Metabolic Modeling

KBase has a suite of Apps supporting the reconstruction, prediction, and design of metabolic models in microbes and plants. Genome-scale metabolic models can be used to explore an organism’s growth in specific media conditions, determine which biochemical pathways are present, optimize production of an important metabolite, identify high flux pathways, and more.

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RNA-seq and Expression Analysis

KBase offers a powerful suite of expression analysis Apps. Starting with short reads, you can use the tool suite to assemble and quantify long transcripts, identify differentially expressed genes, cluster them and analyze them as functionally enriched modules. You can also compare the expression data with the flux when studying metabolic models in KBase and identify pathways where expression and flux agree or conflict.

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Comparative Genomics

KBase provides multiple comparative genomics and phylogenetic analysis Apps to enable researchers to understand evolutionary relationships between organisms and explore structural and functional variance across genomes.

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KBase Tutorial Narratives

These Narrative tutorials provide step-by-step examples that show how to use KBase tools and data to perform useful analyses. You can copy these Narratives and rerun the steps, modify the analyses, or try on your own data.

Made by the KBase Documentation team

KBase provides multiple Apps for de novo assembly of prokaryotic Next-Generation Sequencing (NGS) reads from various sequencing platforms. These assemblies can then be annotated with RAST or Prokka, enabling you to…

Made by the KBase Documentation team

KBase has a suite of tools and data that support the reconstruction, prediction, and design of metabolic networks in microbes. Starting from genome sequence data, this Narrative demonstrates how to use…

Made by Sam Seaver

PlantSEED was designed to streamline the process of annotating plant genome sequences, constructing metabolic models based on genome annotations, and using models to predict gene functions. This Narrative tutorial demonstrates…

Made by Sunita Kumari

KBase’s RNA-seq pipeline uses Tuxedo tools (including Bowtie, TopHat, Cufflinks, Cuffmerge and Cuffdiff) to quantify gene expression from RNA-seq reads. The resulting expression matrix can be used by other KBase…

Made by Dylan Chivian

Gene trees can provide insight when the evolutionary history of a gene family differs from vertical inheritance that tracks with a species tree. This tutorial walks through an example of…

Made by Dylan Chivian

KBase has powerful tools for metabolic modeling and comparative phylogenomics of microbial genomes that can be used for developing a mechanistic understanding of functional interactions between species in microbial ecosystems. Essential…

Upcoming webinars

Upcoming webinars

Learn about using KBase for your systems biology and bioinformatics research with one of our upcoming webinars. All past webinars are also available for viewing.

30
Sep
2020
1 pm ESt
Learn the basics of using KBase and find out how it can help your research. This webinar will introduce users to working in KBase, including data upload, using the Narrative interface, running apps, and sharing your analysis. We’ll also cover any new features and developments to support your research. Find out why KBase is the best way to create personalized, reproducible, shareable bioinformatics workflows. Register for webinar: https://forms.gle/n6HXjg2rRy7dTrQy9 Hosted by Ben Allen, Oak Ridge National Laboratory
Previous webinars

Previous webinars

Aug 19, 2020
In this webinar, we examine two ways that KBase users can use their work in KBase to advance scientific discovery. First, we show KBase features and best practices associated with publishing Narratives, including improving data availability in accordance with FAIR (Findable, Accessible, Interoperable, and Reusable) data principles and utilizing the features of the Narrative interface to improve the impact of the Narratives. Then, we share community resources and features of KBase that make it a valuable tool for educators.
Jul 22, 2020
Genome announcements share and promote newly sequenced organisms with the larger scientific community. A few decades ago, genome announcements were highly anticipated hallmarks of novel science. But, what was once a publishing coup is now an every day event. It is harder and harder to keep abreast of all the genomes that have been sequenced and promote your own new genomes to get the attention and recognition of your research community. Fortunately, KBase can help construct genomes from your sequencing data, generate reports for your announcement, and promote your data to your research community. Join this webinar to learn how to go from sequencing reads to genomes and share your data all within KBase.
Jun 17, 2020
Sean Jungbluth, Lawrence Berkeley National Laboratory KBase provides users with a robust suite of tools to interrogate environmental genome sequence data. This webinar will highlight the application of bioinformatic tools for metagenome assembly and genome binning with an emphasis on the recovery of novel microbial lineages from the deep subseafloor environment. In particular, we will highlight the effective use of employing multiple genome binners and a bin optimization approach. We’ll also show some newly released KBase apps for this approach like our CONCOCT binner and DAS-Tool bin optimizer.
May 20, 2020
Dylan Chivian and Sean Jungbluth, Lawrence Berkeley National Laboratory KBase has powerful tools for analyzing microbial communities and developing an understanding of functional interactions between species in microbial ecosystems. This webinar guides users through the basics of using KBase tools to assemble metagenome sequence data and prepare high-quality bins to use for comparative phylogenomics, metabolic modeling, and more
Apr 22, 2020
Learn how perform whole-genome phylogeny, homology, and domain family functional profiling across a clade of organisms. This webinar will showcase an example of using KBase to analyze gene families and construct gene trees from some Clostridia genomes.
Apr 15, 2020
KBase has powerful tools for analyzing microbial communities and developing an understanding of functional interactions between species in microbial ecosystems. This webinar guides users through the basics of using KBase tools to create community metabolic models to simulate interactions between constituents.
Apr 08, 2020
Learn to use RNA-seq to analyze gene expression patterns across different samples. This webinar will demonstrate how to import reads and a genome, align and assemble transcripts, perform differential expression analysis, and perform QC at various steps of the analysis using KBase.
Apr 01, 2020
Interested in constructing metabolic models from your genomics data? This webinar will introduce participants to the basics of metabolic modeling in KBase. Learn how to annotate genomes, reconstruct metabolic models, and perform flux balance analysis to better understand the metabolic capacity of your organism.
Mar 30, 2020
Learn how to analyze isolate organisms in KBase starting from sequencing data. Attendees will learn how to find data and use tools for quality control and assessment of NGS reads, de novo assembly, genome annotation, and how to analyze features of genomes within KBase.
Mar 11, 2020
Learn how to use advanced KBase Apps for metabolic modeling. Attendees will see some of the newest Apps KBase is developing for metabolic modelings.
Looking for information on tools and resources?

Looking for information on tools and resources?

Check out KBase Documentation for our Getting Started guide and information on tools in the App Catalog. KBase is a fully open source software project available on GitHub.