skDER Representative Genomes for Select Bacterial Taxa

skDER Representative Genomes for Select Bacterial Taxa is a collection of dereplicated bacterial genome assemblies for 18 specific taxa, derived from the GTDB R214 database. The dataset includes representative genomes selected via greedy clustering with skDER at 99% ANI and 90% AF cutoffs, alongside files detailing clustering relationships and taxonomic classifications. It provides a non-redundant genomic resource for comparative studies across genera like Escherichia, Klebsiella, and Acinetobacter.

Use Cases

• Comparative genomic analysis based on representative FASTA sequences for specific bacterial taxa.
• Taxonomic classification validation using the provided GTDB R214 classifications in the overview file.
• Studying genome diversity and dereplication efficiency using the clustering information files.
• Phylogenetic reconstruction of bacterial genera using the selected representative genomes.

Strengths

• Includes explicit counts of representative and total considered genomes for 10 listed taxa, such as 2,436 representative Escherichia genomes from 34,358 total.
• Uses a defined, reproducible methodology with skDER v1.0.7 and specific clustering parameters (99% ANI, 90% AF).
• Provides multiple file types (overview TSV, clustering info, FASTA archives) for different analytical needs.

Limitations

• Incomplete metadata: specific column names, total row counts, dataset size, and precise update dates are not provided.
• The description is truncated, leaving the full list of 18 taxa and potentially other details unknown.
• Relies on a single, potentially outdated database version (GTDB R214).

Provenance

Source

Genomes sourced from GTDB (Genome Taxonomy Database) release R214.

Collection Method

Genomes gathered via loose taxonomic string search and dereplicated using skDER v1.0.7 in greedy clustering mode.