Indexing GlobDB

Info:

GlobDB , a dereplicated dataset of the species reps of the GTDB, GEM, SPIRE and SMAG datasets a lot.
https://x.com/daanspeth/status/1822964436950192218

Data:

# check the latest version here: https://fileshare.lisc.univie.ac.at/globdb/

# download data
wget https://fileshare.lisc.univie.ac.at/globdb/globdb_r220/globdb_r220_genome_fasta.tar.gz

tar -zxf globdb_r220_genome_fasta.tar.gz

# file list
find globdb_r220_genome_fasta/ -name "*.fa.gz" > files.txt

Taxonomy data to limit TaxId in lexicmap search since LexicMap v0.7.1.

wget https://fileshare.lisc.univie.ac.at/globdb/globdb_r220/globdb_r220_tax.tsv

# Create taxdump files with TaxonKit: https://bioinf.shenwei.me/taxonkit/usage/#create-taxdump    
taxonkit create-taxdump -A 1 -R superkingdom,phylum,class,order,family,genus,species globdb_r220_tax.tsv -O taxdump

# It has a file mapping assembly accession to TaxId
ln -s taxdump/taxid.map

Indexing with LexicMap

# elapsed time: 3h:40m:38s
# peak rss: 87.15 GB
lexicmap index -S -X files.txt -O globdb_r220.lmi --log globdb_r220.lmi -g 50000000