Metagenome-assembled Genome Extraction and Analysis

This webinar demonstrates how to extract metagenome-assembled genomes (MAGs) from your microbial community sequencing data. KBase scientist Dylan Chivian demonstrates the workflow from his recently published protocol for extracting MAGs from microbiome data and guide users through some of the analysis tools available on the platform. This process allows scientists to generate putative genomes from organisms found in the environment and understand their functional capacity and their role in the ecosystem.

0:00 Introduction to the webinar and protocol
4:35 Import and read quality
8:14 Read taxonomy - Kaiju
13:23 Metagenome assembly
17:18 Comparing assembled contigs
20:05 Contig binning
22:17 Optimizing binned contigs
25:05 Bin quality assessment
34:33 Extract individual assemblies
35:38 Annotate genomes
36:40 Taxonomic classification of MAGs with GTDBtk
39:30 Finding relatives with Species Tree
42:58 Placing genomes into phylogenetics context with phylum exemplars
44:40 Functional classification of MAGs
46:25 HMMER profiling and gene set extraction
48:00 Summarize GenomeSet

Read and cite the article: https://doi.org/10.1038/s41596-022-00...
Read and cite the Narrative: https://doi.org/10.25982/33233.606/18...

Q&A Doc available here: https://docs.google.com/document/d/1F...