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test_cenote, test_code_prediction, benchmark_markers - test procedures
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run_cenote - run Cenote-Taker 2 for the 4 cohorts
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rrna_NL_vir - detect rRNA genes in the virus-like contigs from the 4 cohorts
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predict_proteomes - predict proteomes for the virus-like contigs from the 4 cohorts
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taxo_NL_vir - assign taxonomy to the virus-like contigs from the 4 cohorts
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get_databases_caudo - detect Caudoviricetes genomes with terminal repeats in 6 databases
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cluster_genomes - dereplicate virus-like contigs from the 4 cohorts and genomes from the databases together (build DB0, DB1)
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map_reads - map reads from the 4 cohorts to DB1
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DEVoC_reads - map reads from the 254 Danish fecal viromes to DB1
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DB2_info, DB3_DB4_info - build DB2, DB3, DB4
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DB3_vConTACT2 - DB3 gene-sharing with TerL-encoding viruses
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DB3_TerL_tree - build & plot phylogenetic tree
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DB3_abundance_stability - % sample reads mapped to DB3 & Bray-Curtis dissimilarity
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DB3_tRNA_scan - tRNA detection in DB3 vOTU representatives
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host_prediction - prophage-, CRISPR- and co-abundance-based host prediction
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DB4_in_GenBank, DB4_in_BanfieldLab - look for phages similar to DB4 vOTU representatives
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DB4_genome_info - nt content & GC skew for extended DB4
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DB4_proteome_annot - functional annotation of proteins encoded by DB4 vOTU representatives
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DB4_genome_maps - plot genome maps of DB4 vOTU representatives
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DB4_pheno_assoc - associations between DB4 vOTUs prevalence and human phenotypes
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workflow_diagram - plot analysis workflow
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blastn_crAss_sensu_stricto - compare MGV-GENOME-0359371 to the first discovered crAssphage
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DEVoC_LoVEphage - LoVEphage in the current study?
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DB0 - 100,060 genomes & contigs pooled together
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DB1 - 30,461 vOTU representatives, result of DB0 dereplication
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DB2 - 15,196 detected vOTU representatives, result of read mapping to DB1
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DB3 - 1,899 DB2 vOTUs represented by Caudoviricetes genomes with terminal repeats
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DB4 - 54 DB4 vOTUs detected in > 5% samples in a Dutch cohort