rpoC Database Downloads
Preformatted Databases
A custom database for your preferred pipeline isn’t here? Open an issue on our github page and we will try to get one added!
📊 DADA2 Reference Sequences
# Download:
wget https://github.com/rpoCdb/rpoCdatabase/blob/main/02-releases/version_2.0/dada2/rpocDB_v2_dada2.fasta.zip
unzip rpocDB_v2_dada2.fasta.zip
# Usage in R:
# assignTaxonomy(..., refFasta="rpocDB_v2_dada2.fasta")
🦠 Kraken2 Custom Database
# Download and build:
wget https://github.com/rpoCdb/rpoCdatabase/blob/main/02-releases/version_2.0/kraken2/rpocDB_v2_kraken2.fasta.zip
unzip rpocDB_v2_kraken2.fasta.zip
kraken2-build --add-to-library rpocDB_v2_kraken2.fasta --db rpocDB_v2_kraken2.db
🔬 mmseqs2 Custom Database
# Download database and taxonomic file:
wget https://github.com/rpoCdb/rpoCdatabase/blob/main/02-releases/version_2.0/mmseqs2/database.fasta.zip
wget https://github.com/rpoCdb/rpoCdatabase/blob/main/02-releases/version_2.0/mmseqs2/mapping.tsv
unzip database.fasta.zip
# Create MMseqs2 sequence database:
mmseqs createdb database.fasta seqTaxDB
# Annotate database with taxonomy:
mmseqs createtaxdb seqTaxDB tmp --tax-mapping-file mapping.tsv --ncbi-tax-dump ncbi_taxdump
# Create index for faster searches:
mmseqs createindex seqTaxDB tmp
# To run taxonomy assignment on a query FASTA file (e.g., query.fasta):
mmseqs createdb query.fasta queryDB
mmseqs taxonomy queryDB seqTaxDB taxonomyResult tmp --lca-ranks superkingdom,phylum,class,order,family,genus,species
mmseqs createtsv queryDB taxonomyResult taxonomy.tsv
mmseqs taxonomyreport seqTaxDB taxonomyResult report.html --report-mode 1
🧫 Mothur Custom Database
# Download database and taxonomy:
wget https://github.com/rpoCdb/rpoCdatabase/blob/main/02-releases/version_2.0/mothur/rpoCdb_v2_mothur.fasta.zip
wget https://github.com/rpoCdb/rpoCdatabase/blob/main/02-releases/version_2.0/mothur/rpoCdb_v2_mothur.taxonomy
unzip rpoCdb_v2_mothur.fasta.zip
🧬 QIIME2-Compatible (.qza/.fasta)
Coming soon!
Metadata
Click here access the taxonomy browser
Download the full metadata file (including ///////) here!
Version History
| Version | Release Date | Changes | Sequence Count |
|---|---|---|---|
| v2.0 | //////////// | ////////////// | 65,156 |
| v1.1 | May 16, 2024 | Updated using GTDB | 42,941 |
| v1.0 | July 10, 2023 | Initial release | 15,690 |