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