Indexing GlobDB
Info:
- GlobDB, a dereplicated dataset of species representatives from the GTDB, GEM, SPIRE, and SMAG datasets.
- https://x.com/daanspeth/status/1822964436950192218
Data:
# check the latest version here: https://fileshare.lisc.univie.ac.at/globdb/
# download data
wget -c https://fileshare.lisc.univie.ac.at/globdb/globdb_r232/globdb_r232_genome_fasta.tar.gz
tar -zxf globdb_r232_genome_fasta.tar.gz
# file list
find globdb_r232_genome_fasta/ -name "*.fa.gz" > files.txt
wc -l files.txt
# 346233 files.txt
Indexing with LexicMap
# elapsed time: 9h:02m:28s
# peak rss: 89.99 GB
lexicmap index -S -X files.txt -O globdb_r232.lmi --log globdb_r232.lmi.log -g 50000000 -b 8000 -j 48
Taxonomy data for filtering by TaxId in lexicmap search since LexicMap v0.8.0.
wget https://fileshare.lisc.univie.ac.at/globdb/globdb_r232/globdb_r232_taxonomy.tsv.gz
# Create taxdump files with TaxonKit: https://bioinf.shenwei.me/taxonkit/usage/#create-taxdump
#
# for older versions with tab-delimited data:
# taxonkit create-taxdump -A 1 -R superkingdom,phylum,class,order,family,genus,species globdb_r220_tax.tsv -O taxdump
#
taxonkit create-taxdump --gtdb globdb_r232_taxonomy.tsv.gz -O taxdump
# It has a file mapping assembly accession to TaxId (below the species rank)
ln -s taxdump/taxid.map
What does the taxdump data look like?
$ echo Escherichia coli | taxonkit name2taxid --data-dir taxdump/
Escherichia coli 599451526
$ echo 599451526 | taxonkit lineage --data-dir taxdump/ -r
599451526 Bacteria;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichia coli species
$ echo 599451526 | taxonkit list --data-dir taxdump/ -nr
599451526 [species] Escherichia coli
1395899945 [no rank] GCF_003697165
$ grep 1395899945 taxdump/taxid.map
GCF_003697165 1395899945
# the number of species
$ echo 1 | taxonkit list --data-dir taxdump/ -I "" | taxonkit filter -E species --data-dir taxdump/ | wc -l
346233
Search in specific taxa.
# a species (Escherichia coli)
lexicmap search -d globdb_r232.lmi -T taxdump/ -G taxdump/taxid.map -t 599451526 b.gene_E_coli_16S.fasta --debug
# a genus (Escherichia)
# echo Escherichia | taxonkit name2taxid --data-dir taxdump/
# Escherichia 1028471294
lexicmap search -d globdb_r232.lmi -T taxdump/ -G taxdump/taxid.map -t 1028471294 b.gene_E_coli_16S.fasta --debug
(last update: 2026-07-02)