nf-core/metatdenovo taxonomy

The data in this repository can be used to assign taxonomy to sequences with Diamond [Buchfink et al. 2015], particularly using the --diamond_dbs parameter in nf-core/metatdenovo (nf-co.re/metatdenovo) , release 1.1 or later.Currently, the data available represents species-representative genomes from the Genome Taxonomy Database (GTDB), release R09-RS220 [Parks et al. 2018]. File preparationAll species-representative genomes from GTDB were downloaded from the National Center for Biotechnology Information (NCBI) and annotated with Prokka [v. 1.14.6; Seemann 2014], and the sequences for all resulting proteins were used for this data.

The taxonomy dump files (in NCBI taxonomy dump format) were created from the GTDB metadata with TaxonKit [v. 0.18.0; Shen and Ren 2021] and the Diamond database with Diamond [v. 2.1.10; Buchfink et al. 2015] in "taxonomy mode", i.e. using the taxonomy dump created with TaxonKit. (See below for commands used.) File descriptionsThere are five files: - gtdb-r220.faa.gz: Fasta file with protein sequences. Not used by nf-core/metatdenovo but can be used to create the Diamond database below. - gtdb-r220.taxonomy.dmnd: Diamond database with taxonomy information. - gtdb-r220.names.dmp: Taxonomy dump file. - gtdb-r220.nodes.dmp: Nodes dump file. - gtdb-r220.seqid2taxid.tsv.gz: Mapping from protein accession to taxon.