Genomes were manually inspected, and we used checkM 2 to see the completeness and contamination scored. See bellow:
The manually curated genomes were de novo reconstructed from high-quality Illumina metagenomic data as described previously
(Chen et al. 2020). From soil samples taken at various depths, we recovered draft illumina-based MAGs corresponding to Atabeyarchaeum
deiteterre and Freyarchaeum
deiteterre. The curation process involved the identification and removal of obvious chimeric regions, which were indicated by abrupt changes in GC content or by insufficient Illumina read mapping support. We also corrected sequences in regions with imperfect read alignment, allowing no single nucleotide polymorphisms (SNPs), by mapping reads at a reduced stringency threshold (allowing for up to 3% SNPs). This was followed by manual curation of the consensus sequence, including insertion, deletion, or substitution of individual base pairs. The extension of contig ends was conducted using unplaced Illumina reads. High read coverage was interpreted as indicative of the genomic termini. A genome was deemed complete when it displayed uninterrupted support from Illumina reads. The final assessment of genome completeness was performed by examining the cumulative GC skew and ensuring alignment with known complete genomes from related taxa. The Average Amino Acids of the new genomes was performed using AAI: Average Amino acid Identity calculator tool (
http://enve-omics.ce.gatech.edu/aai/) and using compareM (v.0.0.23) with the ‘aai_wf’ at default settings (
https://github.com/dparks1134/CompareM) . Replichores of complete genomes were predicted according to the GC skew and cumulative GC skew calculated by the iRep package (gc_skew.py).