Day 3

Github Repositories
Metabolism
Viruses!

Relevant Publications and Resources

Katrina McMahon Lecture
Microbial species delineation using whole genome sequences
Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph
Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria
Bacterial ecology and evolution converge on seasonal and decadal scales
IGV for read visualization – 2nd to Anvi’o
Cultivation and genomics of the first freshwater SAR11 (LD12) isolate

Annotation of Metabolic Genes
Prokka: rapid prokaryotic genome annotation
Github page for Prokka
DRAM for distilling microbial metabolism to automate the curation of microbiome function
Github page for DRAM
Visualization of annotation using KEGG’s Automatic Annotation Server KAAS

Viruses within Microbial SAGs
Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses
Identifying viruses from metagenomic data using deep learning
CheckV assesses the quality and completeness of metagenome-assembled viral genomes
PhANNs, a fast and accurate tool and web server to classify phage structural proteins
mobileOG-db: a Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements
Evaluation of computational phage detection tools for metagenomic datasets
Benchmarking informatics approaches for virus discovery: Caution is needed when combining in silico identification methods