Notebooks supporting the publication:
Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms
All genomes reported in Table 1. are available in the genomes folder (files ending in .fasta) along with predicted proteins (files ending in .faa). More information on genomes in available in the file genomeInfo.csv
Supplemental Figure S1. Dendrogram of reference and de novo assembled C. parapsilosis genomes based on genome-wide average nucleotide identity (ANI).
Supplemental Figure S2. Raw variant frequency graphs used to determine ploidy of all de novo assembled genomes.
Supplemental Figure S3. Determination of aneuploidy for all de novo assembled genomes.
Supplemental Figure S4. Alternative determination of aneuploidy for genomes with high quality reference genomes.
Supplemental Figure S5. Effect of coverage on variant frequency determination as assessed through simulation of metagenomic reads.
Supplemental Figure S6. Evaluation of relative abundance, genome length, and sequencing depth needed to achieve 8x sequencing coverage.
Supplemental Table S1. Sequencing metadata for all infant and room metagenomic samples
Supplemental Table S4. Mapping-based abundance of eukaryote genomes in all samples
Supplemental Table S3. Metadata for statistical associations
Supplemental Table S4. Statistical associations of samples containing eukaryotes with metadata.
Supplemental Table S3 = SampleMetadata_v1.csv
Supplemental Table S4 = MappingListGamma_genomeCoverage_v1.csv