2026-10-14 https://api.researchdata.se/oai-pmh

oai:researchdata.se:doi-10-17044-scilifelab-28211678/0 2025-02-24 subject:ssif:3 subject:ssif:106 subject:ssif:1 subject:ssif:10611 subject:ssif:10609 principal:slug:linnaeus-university

info:eu-repo/semantics/other http://purl.org/dc/dcmitype/Dataset https://doi.org/10.17044/SCILIFELAB.28211678 nf-core/metatdenovo taxonomy https://orcid.org/0000-0002-8779-6464 Medical and Health Sciences Medicin och hälsovetenskap Biological Sciences Biologi Ecology Ekologi Genetics and Genomics Genetik och genomik 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 (https://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. The Diamond database and taxonomy dump files can be used with nf-core/metatdenovo (Version >1.1) by providing a csv file like below to the --diamond_dbs parameter. (Although Nextflow can use https-urls for paths, it is usually better to download the very large files and keep local copies.) db,dmnd_path,taxdump_names,taxdump_nodes,ranks,parse_with_taxdump gtdb,gtdb_r220_repr.dmnd,gtdb_taxdump/names.dmp,gtdb_taxdump/nodes.dmp,domain;phylum;class;order;genus;species;strain, Commands used to prepare taxonomy dump files and the Diamond database- Taxonomy dump: cut -f 1,19-20 *metadata.tsv | grep -v 'accession' | awk 'BEGIN { FS="\t" } { if ( $2 == "t" ) { print $1 "\t" $3 } }' | taxonkit create-taxdump --gtdb -O . - Diamond database: gunzip -c gtdb-r220.faa.gz | sed '/^>/s/ .*//' | diamond makedb --taxonmap gtdb-r220.seqid2taxid.tsv.gz --taxonnames gtdb-r220.names.dmp --taxonnodes gtdb-r220.nodes.dmp --db gtdb-r220.taxonomy.dmnd --no-parse-seqids Revision history20250211 First version https://creativecommons.org/licenses/by/4.0/ Linnaeus University Linnéuniversitetet 2025-02-24T00:00:00Z