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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:
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.App List
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.App List
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.App List
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.App List
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.App List
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.
Learn how to incorporate microbial metagenomic and environmental metabolite data from watershed ecosystems into metabolic and community modeling using computational frameworks in this virtual course.
Join the community of educators using KBase to teach bioinformatics and computational biology!
While KBase is routinely used for advanced analysis by scientists around the world,…
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…
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…
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…
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…
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…
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…
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.
Want to improve metabolic annotations? KBase has new apps to combine multiple functional annotations. Join this webinar to learn about the tools and process in KBase from Patrik D’haeseleer of Lawrence Livermore National Lab. Patrick is part of the Biofuels Scientific Focus Area and has been working with the KBase team to curate more accurate draft metabolic models through developing new tools that improve the quality of annotation.
14 April 2021
1 PM ET / 10 AM PT
Learn about tools for taxonomic profiling in KBase. Join Mark Flynn of Los Alamos National Lab, a developer with the Bacterial-Fungal Interactions Scientific Focus Area. Mark will demonstrate taxonomic profiling for metagenomes using the GOTTCHA2 App he developed for the KBase community.
21 April 2021
1PM ET / 10AM PT
Learn the basics of KBase and how it can help your research. This webinar introduces new users to KBase including data upload, using the Narrative interface, running apps, and sharing…