amdpi: a pipeline for awesome-microbiome-datasets

Goal

Tracking published microbiome datasets

Sequencing data

NCBI SRA
EBI ENA

Taxonomic profiles and metadata

curatedMetagenomicData
curatedFoodMetagenomicData

Genomics catalog

Bacteriome

Human Gut
- UHGG
Human oral
Human skin

Virome

Human Gut
- UHGV
Human oral
Human skin

Benchmark data

CAMI
LMAS Benchmarking metagenomics assembly
Others Benchmarking microbial growth rate predictions from metagenomes

Vitro microbial community

hCom1
hCom2