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New Tutorial: Genome Extraction from Metagenomic Data
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This new Narrative Tutorial guides users through the process of obtaining high-quality genomes from a metagenome assembly and placing them into phylogenetic context. In the tutorial, you will learn how to clean raw metagenomic shotgun sequencing reads, assemble these reads, perform genome binning on these assemblies, and generate annotated genomes and species predictions from these bins. You can also generate taxonomic abundance based on protein similarity from the raw reads using Kaiju app or using annotated genomes to analyze similarity to reference genomes through the creation of phylogenetic species trees. Genome extraction and species prediction are just the beginning of how metagenomic samples can be analyzed within KBase, as these extracted genomes can be used as input for downstream analysis with our powerful tools for metabolic modeling and comparative phylogenomics.
View this Narrative Tutorial on KBase
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DOE Funded Collaborations to Grow KBase
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The Department of Energy recently funded five Science Focus Area (SFA) awards that will provide valuable tools and data directly to our research community through the KBase platform. Awards were made to LBNL, LLNL, LANL, and ORNL, in collaborations with MIT, Ohio State University, and University of California Berkeley. The two-year funded projects range from developing tools that will improve the quality of genomes inferred from metagenomic data (MAGs – Metagenome Assembled Genomes), to allowing users to do protein structure-bases analyses on the KBase platform. Keep watching this newsletter and follow us on social media to stay informed as new data sets and tools come online!
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KBase at AGU Fall 2018 Workshop
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KBase scientist Chris Henry will be among many researchers presenting at the Modeling Microbial Dynamic and Processes from Cells to Ecosystems workshop at the American Geophysical Union Fall Meeting 2018, on December 9 from 8 a.m. to 4 p.m. The workshop focuses on tools for understanding the incorporation of microbial processes in mechanistic models at various levels of complexity using a variety of methods including genome-informed, trait-based, enzyme-based reaction networks, and flux balance analysis. The workshop will start with research presentations from leading pioneers in this field, followed by tutorials and hands-on demonstrations. Bring laptops!
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Recent Publications Using KBase |
Several new publications have been released that showcase the diversity of applications for KBase in genomics research. Check out how scientists are using KBase to explore data, run analyses, and discover new findings.
- Adeniji AA, Aremu OS, Babalola OO. Selecting lipopeptide-producing, Fusarium- suppressing Bacillus spp.: Metabolomic and genomic probing of Bacillus velezensis NWUMFkBS10.5.
MicrobiologyOpen
- Xu X, Zarecki R, Medina S, Ofaim S, Liu X, Chen C, et al. Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions.
The ISME Journal
- Checcucci A, diCenzo G, Ghini V, Bazzicalupo M, Becker A, Decorosi F, et al. Creation and characterization of a genomically hybrid strain in the nitrogen-fixing symbiotic bacterium Sinorhizobium meliloti.
ACS Synthetic Biology
- Cashman M, Cohen MB, Ranjan P, Cottingham RW. Navigating the maze: the impact of configurability in bioinformatics software.
Proceedings of the 33rd ACM/IEEE International Conference on Automated Software Engineeringdoi:10.1145/3238147.3240466 – Link to Publication
- Li W, Li H, Liu Y, Zheng P, Shapleigh JP. Salinity-Aided Selection of Progressive Onset Denitrifiers as a Means of Providing Nitrite for Anammox.
Environmental Science & Technology
- Dobritsa AP, Kutumbaka KK, Samadpour M. Reclassification of Eubacterium combesii and discrepancies in the nomenclature of botulinum neurotoxin-producing clostridia: Challenging Opinion 69. Request for an Opinion.
International Journal of Systematic and Evolutionary Microbiology
- Kumar M, Ji B, Babaei P, Das P, Lappa D, Ramakrishnan G, et al. Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: Lessons from genome-scale metabolic modeling.
Metabolic Engineering
- diCenzo GC, Debiec K, Krzysztoforski J, Uhrynowski W, Mengoni A, Fagorzi C, et al. Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14.
Genes
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KBase SDK Documentation Upgrades
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The KBase Software Development Kit (SDK) is a set of tools for developing KBase apps that can be dynamically registered and run on the KBase. Feedback from external developers about the content of previous SDK trainings led us to overhaul the documentation to address common issues and improve it overall. Check out the new SDK documentation on Github:
https://kbase.github.io/kb_sdk_docs/
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Newsletter #9 |
November 28, 2018 |
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