Cerebus_v2: Microbial Genome Contig Database

Each row in the Cerebus_v2 dataset represents a single contig (contiguous DNA sequence) from a microbial genome. Genomes are organized into three major datasets — GTDB (isolate genomes), IMG/PR (plasmid/phage), and metagenomic (metagenome-assembled genomes from diverse environments). Where available, each contig is annotated with bin-level metadata including the genome_id it belongs to, its taxonomic classification (taxonomy), genome quality scores (completeness and contamination from CheckM), and a species_cluster assignment.

Schema

Column	Type	Description
dataset	string	Top-level dataset (GTDB, IMGPR, metagenomic)
source	string	Data source (e.g. GTDB_r220, NCBI, HumanGut_UMGS, MGnify_chicken_gut)
file	string	Original genome file name
contig	string	Contig header from the FASTA file
sequence	string	Nucleotide sequence
genome_id	string	Genome/bin identifier linking all contigs from the same genome
taxonomy	string	Taxonomic classification (format varies by source)
completeness	float	Genome completeness (%) from CheckM, where available
contamination	float	Genome contamination (%) from CheckM, where available
species_cluster	string	Species cluster representative, where available

Dataset Summary

Dataset	Files	Size	Description
GTDB	36	101 GB	GTDB r220 isolate genomes
IMG/PR	1	4.8 GB	IMG/PR plasmid and phage sequences
Metagenomic	234	636 GB	MAGs from NCBI, UHGG, UMGS, GEM, Youngblut, GPD, and MGnify biome catalogs
Total	271	742 GB

Examples

Metagenomic (Human Gut UMGS source)

Column	Value
dataset	metagenomic
source	HumanGut_UMGS
file	DRR042264_bin.1.fa
contig	NODE_10_length_190864_cov_5.081646
genome_id	DRR042264_bin.1
taxonomy	k__Bacteria;p__Tenericutes;c__Mollicutes;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Solobacterium
completeness	91.98
contamination	1.65

Metagenomic (NCBI source)

Column	Value
dataset	metagenomic
source	NCBI
file	GCF_000003135.1_ASM313v1_genomic.fna
genome_id	GCF_000003135.1
taxonomy	Bifidobacterium longum subsp. longum ATCC 55813

GTDB

Column	Value
dataset	GTDB
source	GTDB_r220
file	GCA_000008085.1_genomic.fna
contig	AE017199.1 Nanoarchaeum equitans Kin4-M chromosome, complete genome
genome_id	GCA_000008085.1_genomic.fna

Usage

import pyarrow.parquet as pq

# Read a single file
table = pq.read_table("GTDB/gtdb_0000.parquet")

# Filter by genome_id to get all contigs from one bin
import pyarrow.compute as pc
mask = pc.equal(table["genome_id"], "GCA_000008085.1_genomic.fna")
genome = table.filter(mask)

File Format

All files are stored as Parquet with zstd compression. The genome_id field links all contigs belonging to the same bin, allowing users to group contigs by genome and access quality and taxonomic annotations at the bin level.