Database for taxonomic assignment of shotgun sequencing reads data

Question

[Muhammad]

Hello everyone.

I was trying to run my raw data from shotgun sequencing through DADA2 and could not find a reference database for the simultaneous taxonomic assignment of all four domains (bacteria, archaea, eukaryota, viruses). The best I could find was 16S database for bacteria and archaea (together in one database) and a separate database for fungi. May be I am looking at it the wrong way or using the wrong tool.

Can someone please suggest a practical solution out of this situation?

Thanks

[Chris Dean]

DADA2 is typically used for the classification of archaea, bacteria and fungi using marker-genes like 16S and ITS. You probably want to check out classifiers that are specific for shotgun metagenomic data like Kraken2 or Metaphlan4. You will find reference database recommendations there too (LChart gives a good one). Good luck.

Answer 1

[LChart]

I'm unsure about pre-built complete databases; but with DADA2 and SHOGUN (and others) you can easily build the database from a fasta and a taxonomy file. Generally one can grab the NCBI taxonomy (https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/) and the RefSeq complete set (https://ftp.ncbi.nlm.nih.gov/refseq/release/complete/) to build a fully comprehensive (but rather massive) nucleotide taxonomy index.