Data required to replicate findings in "Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research"

This repository provides access to all data and code required to replicate findings from the publication Trickovic et al. (2025) "Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research". Since the HumGut catalog is too big to upload here, you can access its metadata at: https://arken.nmbu.no/~larssn/humgut/All_genomes.tsv.There, you can use the links provided to download all of the genomes from their home repositories. Here, you can find the HumSub catalogue itself, available in two versions: 1) HuMSub_51_1000.sbt.zip: Subspecies-specific hashes created based on kmer length of 51 and scaling factor of 1000. It is used for general subspecies quantification; 2) HuMSub_21_1000.sbt.zip: Subspecies-specific hashes created based on kmer length of 21 and scaling factor of 1000. It is used for querying the Mastiff database for studying the biogeographical distribution of subspecies. Finally, you can find simulated metagenomic samples: 1) humgut_samples.tar.gz: Contains ten pair-end simulated sequencing data created using MAGs from the HumGut catalog; 2) new_samples.tar.gz: Contains ten pair-end simulated sequencing data created using MAGs outside the HumGut catalog. All corresponding code can be found at: https://github.com/trajkovski-lab/humsub