Scientific Literature

• Multiple levels of the unknown in microbiome research - A good primer on the field of metagenomics
• Metagenomic Assembly: Overview, Challenges and Applications - Another good overview of the field of metagenomics
• Quick insights from sequencing data with sourmash - A tutorial and explanation of sourmash, including a definition of k-mers, computing sourmash signatures, comparing RNA-seq samples quickly, detecting eukaryotic contamination in raw RNA-seq reads, building your own database for searching, and other sourmash databases.
• Large-scale sequence comparisons with sourmash - Background on the theory of different commands included in sourmash, accompanied by three small tutorials
• Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity - First spacegraphcats publication that details metagenome-assembled genome bin completion via assembly graph queries.
• Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs - Describes the dataset used in the spacegraphcats publication. Uses a typical de novo metagenomics workflow.
• Streamlining Data-Intensive Biology With Workflow Systems - A primer on using workflow systems for data-intensive biology, and other tips and tricks for working with large volumes of biological data