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Table 3 Coverage-based binning can enhance the recovery of individual genomes from metagenomes

From: A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes

Abundance class (Bin #) % Binned reads in global assembly % Binned reads from “key player” Bin coverage (estimated by CB-Cl) Bin coverage measured (from read mapping) Bin size (estimated by CB-Cl) Bin size measured (assembly length) %Reads used in assembly of individual bins
Bin I 0.2 % 91.3 % 581 656 6.8 Mbp 6.5 Mbp 91.3 %
Bin II 0.5 % 1.3 % 317 306 7.0 Mbp 8.9 Mbp 86.3 %
Bin III 1.6 % 0.0 % 140 152 20.4 Mbp 21.2 Mbp 86.2 %
Bin IV 49.8 % 0.0 % 47 44 38.9 Mbp 37.6 Mbp 71.4 %
Bin V 37.7 % 0.0 % 14 17 117 Mbp 39 Mbp 30.4 %
  1. Raw reads generated from a poly-aromatic hydrocarbon degrading enrichment culture [18] were assembled (with the ALLPATHS program [20]) globally on one hand, and segregated into 5 abundance classes (bins) followed by targeted assembly of reads from individual classes on the other hand. The assembly of reads with the highest coverage (Bin I) led to the reconstruction of a single 6.5 Mbp genome (key player), which is missing in the global metagenome assembly