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databases.md

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Currently available Phanta databases

Name/Link Prokaryotic Portion Viral Portion Prophage-masked? Taxonomy for Prokaryotic Portion Comments
Default database HumGut MGV + RefSeq viral N NCBI Default database (as described in our manuscript)
Masked version of default database HumGut MGV + RefSeq viral Y NCBI Prophage-masked version of default database (as described in our manuscript)
Default database - GTDB HumGut MGV + RefSeq viral N GTDB Default database with GTDB taxonomy for prokaryotic portion
UHGGV2 + MGV UHGGV2 MGV + RefSeq viral N GTDB Default database with UHGGv2 replacing HumGut. UHGGv2 includes low-prevalence prokaryotes filtered by HumGut
HumGut + UHGV "MQ+" HumGut UHGV ($\ge$ medium-quality genomes) N NCBI Same as default database but replacing the viral portion with new viral genome catalog UHGV. Here we included UHGV genomes $\ge$ medium-quality
HumGut + UHGV "HQ+" HumGut UHGV ($\ge$ high-quality genomes) N NCBI Same as previous line but using only $\ge$ high-quality UHGV genomes
UHGGv2 + UHGV "MQ+" UHGGV2 UHGV ($\ge$ medium-quality genomes) N GTDB UHGGv2 for prokaryotic portion; UHGV for viral portion ($\ge$ medium-quality genomes)

Each database should include the following files:

Kraken2 database

  1. hash.k2d
  2. taxo.k2d
  3. opts.k2d
  4. seqid2taxid.map

Bracken databases (built for use with various read lengths N):

  1. databaseNmers.kmer_distrib

Additional files required for pipeline to run:

  1. inspect.out
  2. taxonomy/nodes.dmp
  3. taxonomy/names.dmp
  4. library/species_genome_size.txt

For use with post-processing scripts:

  1. host_prediction_to_genus.tsv
  2. species_name_to_vir_score.txt

Note: Phanta was developed with human gut metagenomes in mind. Phanta's default database was built based on human-gut viral and bacterial genomes. If you wish to apply Phanta on non human gut metagenomes you'll probably need to supply a custom database. In such cases please open new discussion and we can discuss the best way to help/collaborate on that.

The total tar.gz file should be about 20-25 GB (depends on the exact version).