KBase Documentation
  • KBase Documentation
  • KBase Terms & Conditions
  • Getting Started
    • Signing Up and Signing In
      • Step-by-Step Signup Guide
      • Authentication Update
    • Supported Browsers
    • Narrative Quick Start
    • Narrative Interface User Guide
      • Access the Narrative Interface
      • Tour the Narrative Interface
      • Narrative Navigator
      • Create a Narrative
      • Explore Data
      • Add Data to Your Narrative
      • Browse KBase Analysis Tools
      • Analyze Data Using KBase Apps
      • Job Browser
      • Revise Your Narrative
      • Format Markdown Cells
      • Share Narratives
      • Linking Static Narratives to ORCID
      • Access and Copy Narratives
      • Organizations
    • FAQs
  • Manage Your Account
    • Linking Accounts
    • Linking KBase to ORCiD
  • Working with Data
    • Data Upload and Download Guide
      • Data Types
      • Importing Data
        • Bulk Import Limitations
      • Assembly
      • Genome
      • FASTQ/SRA Reads
      • Flux Balance Analysis (FBA) Model
      • Media
      • Expression Matrix
      • Phenotype Set
      • Amplicon Matrix
      • Chemical Abundance Matrix
      • SampleSet
      • Compressed/Zipped Files
      • Bulk Import Specification
      • Downloading Data
    • Searching, Adding, and Uploading Data
    • Filtering, Managing, and Viewing Data
    • Linking Metadata
      • Ontologies and Validated Terms
    • Public Data in KBase
    • Transfer Data with Globus
  • Using Apps
    • Analysis Apps in KBase
      • Assembly & Annotation
      • Comparative Genomics
      • Metabolic Modeling
      • Metagenomics & Community Exploration
      • Data Matrices - Amplicon, Stats
      • Chemical Abundance
      • Expression & Transcriptomics
    • Apps in Beta
  • Running Common Workflows
    • Assembling & Annotating Microbial Genomes
      • FAQ: Assembly and Annotation
    • Comparative Genomics & Phylogenetic Analysis
      • FAQ: Comparative Genomics
    • Metagenomic & Community Analysis
      • FAQ: Metagenomics & Community Analysis
    • Transcriptomic Analysis
      • FAQ: RNA-seq Analysis
    • Constructing Metabolic Models
      • Constructing and Analyzing Metabolic Flux Models of Microbial Communities
      • FAQ: Metabolic Modeling
  • Community Developed Workflows and Tools
    • Functional Annotation
    • Functional and Taxonomic Profiling of MAGs
    • Taxonomy
    • Viral
    • Random Walk with Restart Toolkit
  • Troubleshooting
    • Problems with the User Interface
    • Help Board
    • How to Report Issues
    • Job Errors and Their Meanings
      • Common Job Errors
        • The Job Log
      • Import Job Errors
      • Assembly App Errors
      • Annotation App Errors
      • Functional Genomics App Errors
      • Modeling App Errors
  • Developing Apps
    • The KBase SDK
    • Create a KBase Developer Account
    • KBase GitHub Repository
  • External Links
    • KBase Narrative Interface
    • KBase web site
    • KBase App Catalog
  • kbase.us
Powered by GitBook
On this page
  • Apps
  • Inputs
  • Narratives
  • Tutorial webinar
  • SFA Collaboration Page

Was this helpful?

  1. Community Developed Workflows and Tools

Functional and Taxonomic Profiling of MAGs

These tools allow users to examine the genetic potential of a community and investigate the strain frequencies of subpopulations in those communities.

PreviousFunctional AnnotationNextTaxonomy

Last updated 7 months ago

Was this helpful?

Apps

  • : Identify polymorphisms within microbiome read sequences against reference genomes.

    • : Map reads to a reference genome.

    • : identify single nucleotide polymorphism (SNP) variants based on mapped reads.

  • : Determine strain genome sequences from sub-populations of allele frequency.

  • : Generate a functional profile of nitrogen cycle genes or universal single-copy markers for metagenomic read libraries and assembled genomes.

Inputs

These apps take metagenome-assembled genomes (MAGs) as objects input. See for an overview of metagenomic workflows.

Narratives

  • – provides an example of the workflow using MAGs

    • Tian et al. (2020) Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity. Microbiome 8:51.

    • Narrative created and made public by Alexey Kazakov, Lawrence Berkeley National Laboratory

  • – guidance for creating MAGs.

Tutorial webinar

SFA Collaboration Page

These apps were developed as part of the Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) Science Focus Area (SFA). To learn more about this collaboration, see: .

Meta-Decoder Call Variants
Map Reads to Reference Sequence
Call Microbial SNPs
StrainFinder v1
strainFinder Repository
FamaProfiling
Fama Read Profiling
Fama Genome Profiling
Genome
Metagenomic and Community Analysis
Groundwater MAGs from Tian et al., 2020
https://doi.org/10.1186/s40168-020-00825-w
Metagenome-Assembled Genome Extraction from a Compost Microbiome Enrichment
https://www.kbase.us/research/adams-sfa/
Tutorial webinar presented by by John-Marc Chandonia (Lawrence Berkeley National Laboratory), Alexey Kazakov (Lawrence Berkeley National Laboratory), and Anni Zhang (Massachusetts Institute of Technology)