Day 2

Github Repositories
Read Recruitment
Read Classification using SAGs

Relevant Publications and Resources

Giovanonni Lecture

• Cultivation of marine bacteria of the SAR202 clade
• SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter
• Biochemical Barriers on the Path to Ocean Anoxia?
• A Timeline of Bacterial and Archaeal Diversification in the Ocean
• Pangenomics Analysis Reveals Diversification of Enzyme Families and Niche Specialization in Globally Abundant SAR202 Bacteria

Metagenomic Read Recruitment to SAGs

• Github page for in-house read recruitment workflow sag-mg-recruit
  • Above workflow developed for: Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation
  • And also used for: Charting the Complexity of the Marine Microbiome through Single-Cell Genomics
• Github page for CoverM
• Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

Parks Lecture

• GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
• Github page for GTDB-Tk
• Proposal for a standardized temporal scheme of biological classification for extant species
• A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
• SeqCode initiative

GORG Classifier

• Assembling the Marine Metagenome, One Cell at a Time
• Improved metagenomic analysis with Kraken 2
• Fast and sensitive taxonomic classification for metagenomics with Kaiju
• Decoupling of respiration rates and abundance in marine prokaryoplankton
• Github page for the GORG-classifier