dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

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DRAM for distilling microbial metabolism to automate the curation of microbiome function (2020, methodology): “We recovered 135 MAGs from this sample, that were dereplicated into 76 medium and high quality MAGs (60).”
iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria (2023, neutral): “2.2 [59] with cutoffs of 90% ANI and 60% coverage.”
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses (2020, methodology): “1 (39) was used to group the 2059 giant virus bins (module dereplicate, option –ignoreGenomeQuality) into 2010 vOTUs.”