Public metagenome datasets annotated using SingleM

These data underlie the community profiles shown at https://sandpiper.qut.edu.au The community profiles are in "unfilled SingleM condensed" format. You may wish to convert them to use relative abundances, etc. using singlem summarise --output-taxonomic-profile-with-extras, which operates without loading the entire profile into memory (unlike some other conversions of the summarise command). For more details and information, see https://wwood.github.io/singlem/tools/summarise. As well as this, metadata files are provided, which contain the following columns (all are one run per row in the TSV/CSV) parsed_metadata: run latitude longitude depth temperature collection_year collection_month per_acc_summary: sample (i.e. run) root_coverage (total coverage of prokaryotes) species_coverage (coverage assigned to the species level) top1_order_fraction (fraction of coverage assigned to the most common order out of the total coverage assigned to order level) top3_order_fraction (total fraction of coverage assigned to the 3 most common orders out of the total coverage assigned to order level) low_complexity (yes/no/missing: yes if top1_order_fraction is > 95%, indicating that the sample may not be a true microbial community) known_species_fraction (coverage assigned to the species level compared to root_coverage, as a %) bacterial_archaeal_bases (estimated number of bases in reads that are prokaryotic, from SPF) metagenome_size (bp) singlem prokaryotic fraction (SPF) average_bacterial_archaeal_genome_size (AGS of prokaryotes) warning (whether singlem prokaryotic_fraction raised a warning) prediction (euk-host-associated or not? An ML prediction) host_or_not (annotated euk-host-association from the "organism" field if possible, or failing that, the ML prediction thereof) organism (official metadata of biosample) kingfisher_metadata: A tab-separated file containing biosample-related metadata downloaded for each run, generated using kingfisher annotate. It has many columns, because every submitter can create new kinds of metadata. Changelog version 2.0.1 Fixed formatting and data in GTDB community profiles. All other data is unchanged (thanks to Cliff Bueno de Mesquita for spotting the issue), version 2.0.0 Additional public metagenomes analysed = 205,695, total metagenomes screened -> 913,165. Integration of GTDB R232 community profiles. Addition of low complexity flags to samples (yes/no). Metadata annotations procured using Kingfisher on 14th May, 2026. Raw metagenomes up to 3rd March, 2026 were screened. GlobDB profiles have not yet ben updated for GTDB R232, so these community profiles remain unchanged. version 1.1.10 Bugfix for host_or_not field affecting a minority of samples (Thanks Donovan Parks) version 1.1.9 Addition of GlobDB R226-based profiles. GTDB-based profiles are the same as in version 1.0.0 No new public metagenomes were analysed. version 1.1.0 Addition of GlobDB R226-based profiles. GTDB-based profiles are the same as in version 1.0.0 No new public metagenomes were analysed. version 1.0.0 Public metagenomes published before Feb 20, 2025 were analysed using SingleM pipe v0.18.3 (the default R220 metapackage), and then renewed using an R226 metapackage (S5.4.0.GTDB_r226.metapackage_20250331). version 0.3.0 Update profiles to use GTDB R220, generated using SingleM renew v0.17.0. version 0.2.0 Initial version. Created using a GTDB R214-based reference SingleM metapackage S3.2.1.GTDB_r214.metapackage_20231006 based on public datasets available Dec 15, 2021.