FMGC Eukaryotic bins and viral contigs

<i>The detection of eukaryotic genomes involved an initial filtration step using EukRep v0.6.772 to selectively retain bins containing substantial amounts of eukaryotic DNA. Bins with more than 1 Mbp of eukaryotic bases were considered as potential eukaryotic bins. Next, Busco v5.5.0 was used to estimate bin completeness and contamination. We obtained a total of 35 putative eukaryotic bins with very low completeness, ranging from 1% to 50%, suggesting no useful eukaryotic genomes could be identified in our dataset. Notably, only 2 bins reached 50% completeness (50.6% and 54.5%).</i><i>Additionally, VirSorter2 (--min-score 0.7) was used to identify viral contigs. Contigs with VirSorter2 score over 0.7 were considered as viral contigs. As short contigs may only represent fragments of viral genomes, contigs that were longer than 5 kb were kept for further analysis. The kept dataset was dereplicated using CD-HIT (v4.8.1, parameters: -c 0.95 -n 8) using a global identity threshold of 95%. We obtained a total of 21,777 non-redundant viral contigs. The completeness and contamination were estimate with CheckV. In total, 2,417 (9.86%) and 165 (0.76%) viral contigs were considered complete or high-quality (&gt;90% completeness).</i>