Alteromonas Digital Organism: Pangenome Databases

C-CoMP's Alteromonas Digital Organism database provides a reproducible pangenome built from multiple genomes using the anvi'o platform. The resource includes core gene sets, phylogenetic trees, and genome similarity assessments for comparative genomic analysis. It represents a collaborative effort between MIT researchers and the Meren and Moran labs.

Use Cases

• Phylogenetic analysis based on RAxML trees and core gene sets.
• Comparative genomics using the pangenome database and contigs files.
• Reproducible workflow execution following the detailed markdown documentation.
• Genome similarity assessment using the provided ANI (Average Nucleotide Identity) output files.

Strengths

• Includes multiple versions (v1.1, v2.1.1) indicating iterative development and updates.
• Provides a reproducible workflow document detailing the creation process from fasta files.
• Contains multiple data artifacts like phylogenetic trees, core protein files, and genome similarity assessments.

Limitations

• Key metadata like row count, file size, and specific last updated dates are missing from all sources.
• Column names and detailed schema for the core databases are not provided.
• Sources describe different versions (v7.1 vs. anvio-dev) but do not clarify the current or definitive state.

Provenance

Source

Massachusetts Institute of Technology (Michelle DeMers, Rogier Braakman), Meren Lab, Moran Lab.

Collection Method

Genomes were processed and pangenome constructed using the anvi'o software platform.