Bacterial-Fungal Interactions SFA

Integrating fungal computational sequence data analysis capabilities

 

 

 

 

 

The Bacterial-Fungal Interactions Science Focus Area (SFA) driven by Patrick Chain at Los Alamos National Laboratory (LANL) aims to address some of the knowledge gaps around bacterial-fungal interactions within the soil. The researchers are using a multi-omics approach to gain a predictive understanding of the bacterial-fungal interactions. This work will shed light on how microbial interactions in soil affect ecosystem services such as plant productivity, nutrient cycling, and carbon flux.

Collaborative Development Object

Data analysis modules:

  • Bulk retrieval of fungal sequencing data, from raw data to draft contigs to finished genome
  • Determination of unique genomic signatures at each taxonomic rank for fungal genomes
  • Specific detection of microbial species based on unique fungal signatures

Tools:

  • GOTTCHA2 (Genomic Origin Through Taxonomic Challenge): This App uses a novel taxonomic profiling method for metagenomes that is both gene-independent and signature-based. It significantly reduces false discovery rates (FDR). (KBase version: Released) 
  • Centrifuge Taxonomic Classifier: This App enables rapid, accurate, and sensitive labeling of metagenomic reads and quantification of species. (KBase version: Beta App)
  • Kraken2 Taxonomic Classifier: This App examines the k-mers within a query sequence and maps k-mers to the lowest common ancestor (LCA) of all genomes in the reference database known to contain a given k-mer.

Additional Information

Meet the Members

SFA Manager/PI: Patrick Chain1
KBase Contact: Paramvir Dehal5,6
Lead Developers: Mark Flynn1 and Chien-Chi Lo1
Project Team: David Bruce1, Jean Challcombe1, James Werner1, Armand Dichosa1, Po-E Li1, Migun Shakya1, Geoffrey House1, Jamey Young2, Pilar Junier3, Debora Rodrigues4
Affiliations: 1Los Alamos National Laboratory, 2Vanderbilt University, 3University of Neuchâtel, Switzerland, 4University of Houston, 5Lawrence Berkeley National Laboratory, 6KBase

Resources

Data center network maintenance 1/22-1/23

Update Jan 19: we have been told that different network maintenance will be performed over the weekend of January 22-23.  We have not been told an exact time, nor whether there will be an outage, nor a duration of any possible outages.  We will continue to post updates if we get them.

Our data center will be performing network maintenance on Monday, January 24, 2022.  This outage should last approximately 10 minutes, and will cause disruption to narrative.kbase.us, appdev.kbase.us, and possibly compute jobs.  We have not yet been notified of a specific time, if we are told a time we will update this message.

Holiday reduced support

The KBase helpdesk will have limited or no staff during the last two weeks of the year (Dec. 20-Jan. 1). There will be delays in responding to tickets.