Extracting closed genomes from comammox enrichment cultures using Nanopore sequencing
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Nitrification is a step within the nitrogen cycle (Figure 1) in which ammonium is oxidized over nitrite to nitrate. Until recently this process was considered to be a two-step reaction performed by two distinct groups of organisms, ammonia oxidizing microorganisms and nitrite-oxidizing bacteria. The recently discovered group of complete ammonium oxidizers (comammox) are capable of performing complete nitrification on their own [1,2]. The lack of comammox pure cultures and the resulting lack of closed, high quality genomes is hindering the study of comammox bacteria. Combining the advantages of long read Nanopore sequencing and high accuracy Illumina read data, this study aims on obtaining closed high quality comammox genomes from enrichment cultures.