Themisto v3 Index: 640k Bacterial Genomes with Species Colors

University of Helsinki researcher Jarno Alanko provides a Themisto v3 colored k-mer index for 639,981 high-quality bacterial genomes. The index contains 71 billion distinct 31-mers, each annotated with one of 2340 distinct species identifiers. This resource enables sensitive pseudoalignment of sequencing reads against a large collection of bacterial genomes.

Use Cases

• Perform pseudoalignment of sequencing reads against bacterial genomes based on the described k-mer index.
• Estimate species abundances in metagenomic samples based on pseudoalignment data using the recommended mSWEEP tool.
• Identify which bacterial species a read is compatible with based on the annotated k-mer colors.
• Map species identifiers to taxonomic names using the provided color_names.csv file.

Strengths

• Indexes 639,981 high-quality bacterial genomes from a curated source dataset.
• Contains 71 billion distinct 31-mers, providing a detailed representation of genomic sequence space.
• Annotates k-mers with 2340 distinct species identifiers, enabling species-level resolution.

Limitations

• Description metadata is limited; actual data quality requires manual inspection after download.
• Column-level documentation is absent; field semantics must be inferred after download.
• Last update date is unknown; freshness unverified.

Provenance

Source

Constructed from the 661k bacterial genomes dataset of Blackwell et al. (PLoS Biology, 2021).

Collection Method

Built with Themisto v3.0.0 using specific command-line parameters detailed in the description.