DOI: 10.5281/zenodo.18603714
title: Data used for Benchmarking Cenote-Taker 3

description: data
|____discovery
| |____ERR10905741
| | |____ERR10905741_myloasm_1a.circ.fna
| | |____genomad
| | | |____genomad_only_contigs.txt
| | | |____ERR10905741_myloasm_1a.circ_with_dtr_virus_genes.tsv
| | | |____ERR10905741_myloasm_1a.circ_with_dtr_virus_summary.tsv
| | |____phold_annotations
| | | |____phold_ERR10905741_gnmd
| | | | |____phold_all_cds_functions.tsv
| | | | |____phold_per_cds_predictions.tsv
| | | |____phold_ERR10905741_ct3
| | | | |____phold_all_cds_functions.tsv
| | | | |____phold_per_cds_predictions.tsv
| | | | |____fails.tsv
| | |____ct3
| | | |____ct3_ERR10905741_1b_virus_summary.tsv
| | | |____ct3_only_contigs.txt
| | | |____ct3_ERR10905741_1b_prune_summary.tsv
| | | |____final_genes_to_contigs_annotation_summary.tsv
| | |____contigs
| | | |____ERR10905741_unique_calls.genomad.fna
| | | |____ERR10905741_unique_calls.ct3.fna
| |____short_read_assemblies
| | |____VLP_samples
| | | |____ERR8081307.ct3_only_contigs.txt
| | | |____ERR8081362.gnmd_only_contigs.txt
| | | |____ERR8081362.ct3_only_contigs.txt
| | | |____ERR8081370.ct3_only_contigs.txt
| | | |____genomad
| | | | |____ERR8081307.contigs_virus_summary.tsv
| | | | |____ERR8081370.contigs_virus_summary.tsv
| | | | |____ERR8081362.contigs_virus_summary.tsv
| | | |____ERR8081370.contigs.fa
| | | |____ERR8081370.gnmd_only_contigs.txt
| | | |____ERR8081307.gnmd_only_contigs.txt
| | | |____ERR8081362.contigs.fa
| | | |____ct3
| | | | |____ERR8081307_ct3_virus_summary.tsv
| | | | |____ERR8081307_ct3_prune_summary.tsv
| | | | |____ERR8081362_ct3_virus_summary.tsv
| | | | |____ERR8081370_ct3_prune_summary.tsv
| | | | |____ERR8081362_ct3_prune_summary.tsv
| | | | |____ERR8081370_ct3_virus_summary.tsv
| | | |____ERR8081307.contigs.fa
| | |____bulk_wgs_samples
| | | |____SRR36807671.contigs.fa
| | | |____ERR13455686.ct3_only_contigs.txt
| | | |____SRR36807671.ct3_only_contigs.txt
| | | |____genomad
| | | | |____ERR13455686.contigs_virus_summary.tsv
| | | | |____SRR36807671.contigs_virus_summary.tsv
| | | | |____SRR36931851.contigs_virus_summary.tsv
| | | |____SRR36807671.gnmd_only_contigs.txt
| | | |____SRR36931851.gnmd_only_contigs.txt
| | | |____ERR13455686.gnmd_only_contigs.txt
| | | |____ERR13455686.contigs.fa
| | | |____SRR36931851.contigs.fa
| | | |____SRR36931851.ct3_only_contigs.txt
| | | |____ct3
| | | | |____ERR13455686_ct3_virus_summary.tsv
| | | | |____SRR36931851_ct3_virus_summary.tsv
| | | | |____ERR13455686_ct3_prune_summary.tsv
| | | | |____SRR36931851_ct3_prune_summary.tsv
| | | | |____SRR36807671_ct3_prune_summary.tsv
| | | | |____SRR36807671_ct3_virus_summary.tsv
| |____DRR290133
| | |____genomad
| | | |____DRR290133_myloasm_1a.circ_with_dtr_virus_genes.tsv
| | | |____DRR290133_myloasm_1a.circ_with_dtr_virus_summary.tsv
| | | |____genomad_only_contigs.txt
| | |____phold_annotations
| | | |____unique_calls_genomad
| | | | |____phold_run_1751497002.788138.log
| | | | |____phold_aa.fasta
| | | |____ct3_DRR290133_1b_294_phold1
| | | | |____phold_all_cds_functions.tsv
| | | | |____phold_per_cds_predictions.tsv
| | | |____phold_DRR290133_genomad1
| | | | |____phold_all_cds_functions.tsv
| | | | |____phold_per_cds_predictions.tsv
| | | |____phold_DRR290133_ct3_1
| | | | |____phold_all_cds_functions.tsv
| | | | |____phold_per_cds_predictions.tsv
| | |____ct3
| | | |____ct3_only_contigs.txt
| | | |____ct3_DRR290133_1b_prune_summary.tsv
| | | |____ct3_DRR290133_1b_virus_summary.tsv
| | | |____final_genes_to_contigs_annotation_summary.tsv
| | |____contigs
| | | |____DRR290133_unique_calls.genomad.fna
| | | |____genomad_only_contigs.txt
| | | |____ct3_only_contigs.txt
| | | |____DRR290133_myloasm_1a.circ.fna
| | | |____DRR290133_unique_calls.ct3.fna
| |____refseq
| | |____refseq_virus_AA_20260107.fasta
| | |____refseq_virus_genomes_20260107.fasta
| | |____blastDBs
| | | |____refseq_AA.pdb
| | | |____refseq_AA.phr
| | | |____refseq_AA.pot
| | | |____refseq_AA.pto
| | | |____refseq_AA.ptf
| | | |____refseq_AA.psq
| | | |____refseq_AA.pin
| | | |____refseq_AA.pjs
| | |____refseq_virus_metadata_20260107.tsv
| |____large_metagenome
| | |____large_meta_resource_testing_metrics.xlsx
|____annotation
| |____hmms
| | |____pharokka_phrogs_consensus.names.tsv
| | |____metc_pgap_consensus.faa
| | |____ct3_v311_virion_consensus.faa
| | |____metc_cog_consensus.faa
| | |____metc_phrog_consensus.faa
| | |____metc_vog_consensus.faa
| | |____ct2_all_consensus.faa
| | |____metc_GVDB_consensus.faa
| | |____all_metc_consensus.faa
| | |____ct2_specific_consensus.faa
| | |____ct3_v311_useful_models_consensus.faa
| | |____ct2_rna_consensus.faa
| | |____all_ct3_consensus.names.tsv
| | |____ct3_v311_dnarep_consensus.faa
| | |____metc_PVOG_consensus.faa
| | |____all_ct3_consensus.VS.ct2_all.mmseqs1.tsv
| | |____all_ct3_consensus.VS.metc.tsv
| | |____all_ct3_consensus.VS.pharokka.tsv
| | |____ct3_v311_rdrp_consensus.faa
| | |____pharokka_phrogs_consensus.faa
| | |____metc_tigr_consensus.faa
| | |____ct3_v311_phrogs_consensus.faa
| | |____ct2_useful_consensus.faa
| | |____all_metc_consensus.names.tsv
| | |____genomad_consensus.faa
| | |____all_ct3_consensus.faa
| | |____all_ct3_consensus.VS.genomad.mmseqs1.tsv
| | |____metc_kofam_consensus.faa
| | |____metc_pfam_consensus.faa
| |____seawater_rna_virome
| | |____phold
| | | |____phold_per_cds_predictions.tsv
| | |____genomad
| | | |____hq_complete_genomes.PRJNA605028_genes.tsv
| | |____AAs
| | | |____PRJNA605028.AA.lengths.tsv
| | | |____PRJNA605028.AA.VS.refseq_virus_AA_20260107.tsv
| | | |____PRJNA605028.AA.faa
| | |____pharokka
| | | |____pharokka_cds_final_merged_output.tsv
| | |____ct3
| | | |____ct3_PRJNA605028_a_virus_summary.tsv
| | | |____final_genes_to_contigs_annotation_summary.tsv
| | |____contigs
| | | |____hq_complete_genomes.PRJNA605028.fna
| | |____metc
| | | |____final_annotation_summary.tsv
| |____gut_dtrs
| | |____gut_dtr_pairwise_fisher.csv
| | |____phold
| | | |____phold_per_cds_predictions.tsv
| | |____genomad
| | | |____gut_dtr_head_tail_contigs1_genes.tsv
| | | |____gut_dtr_head_tail_contigs1_taxonomy.tsv
| | |____AAs
| | | |____gut_dtr_head_tail_AA.faa
| | | |____gut_dtr_head_tail_AA.VS.refseq_virus_AA_20260107.tsv
| | | |____gut_dtr_head_tail_AA.lengths.tsv
| | |____gut_dtr_perfect_stats.csv
| | |____gut_dtr_per_gene_stats.csv
| | |____pharokka
| | | |____pharokka_cds_final_merged_output.tsv
| | |____gut_ct3_vs_genomad
| | | |____gut_ct3_vs_genomad.nb.html
| | | |____ct3_genomad_virion_disagree1.tsv
| | | |____gut_ct3_vs_genomad.Rmd
| | | |____ct3_genomad_annotation_compare.tsv
| | | |____gut_dtr_ct3_virion_contigs_genes.tsv
| | | |____final_genes_to_contigs_annotation_summary.tsv
| | |____ct3
| | | |____ct3_g_dtr_ht_1b_virus_summary.tsv
| | | |____final_genes_to_contigs_annotation_summary.tsv
| | |____contigs
| | | |____gut_dtr_head_tail_contigs.txt
| | | |____gut_dtr_head_tail_contigs1.fna
| | |____metc
| | | |____final_annotation_summary.tsv
| |____uhgv
| | |____phold
| | | |____phold_per_cds_predictions.tsv
| | |____genomad
| | | |____first_100_uhgv_votus_taxonomy.tsv
| | | |____first_100_uhgv_votus_genes.tsv
| | |____pipeline_time_data1.xlsx
| | |____pharokka
| | | |____pharokka_cds_final_merged_output.tsv
| | |____ct3
| | | |____ct3_uhgv100_1a_virus_summary.tsv
| | | |____final_genes_to_contigs_annotation_summary.tsv
| | |____contigs
| | | |____first_100_uhgv_votus.fna
| | | |____first_1000_uhgv_votus.fna
| | |____metc
| | | |____final_annotation_summary.tsv
| |____seawater_dtrs
| | |____seawater_dtr_per_gene_stats.csv
| | |____phold
| | | |____phold_per_cds_predictions.tsv
| | |____seawater_dtr_perfect_stats.csv
| | |____genomad
| | | |____seawater_dtr_headtail_contigs_genes.tsv
| | | |____seawater_dtr_headtail_contigs_taxonomy.tsv
| | |____AAs
| | | |____seawater_dtr_headtail_AA.VS.refseq_virus_AA_20260107.tsv
| | | |____seawater_dtr_headtail_AA.faa
| | | |____seawater_dtr_headtail_AA.lengths.tsv
| | |____seawater_dtr_pairwise_fisher.csv
| | |____pharokka
| | | |____pharokka_cds_final_merged_output.tsv
| | |____ct3
| | | |____ct3_s_dtr_ht_1a_virus_summary.tsv
| | | |____final_genes_to_contigs_annotation_summary.tsv
| | |____contigs
| | | |____seawater_dtr_headtail_contigs.fna
| | | |____seawater_dtr_headtail_contigs.txt
| | |____sea_ct3_vs_genomad
| | | |____sea_ct3_vs_genomad1.nb.html
| | | |____sea_ct3_vs_genomad1.Rmd
| | | |____ct3_genomad_virion_disagree1.tsv
| | | |____seawater_dtr_ct3_virion_contigs.fasta
| | | |____seawater_dtr_ct3_virion_contigs_genes.tsv
| | | |____ct3_genomad_annotation_compare.tsv
| | | |____final_genes_to_contigs_annotation_summary.tsv
| | |____metc
| | | |____final_annotation_summary.tsv
| |____refseq
| | |____genomad
| | | |____refseq_virus_genomes_20260107_genes.tsv
| | |____pharokka
| | | |____pharokka_cds_final_merged_output.tsv
| | |____ct3
| | | |____ct3_refseq_an2_virus_summary.tsv
| | | |____final_genes_to_contigs_annotation_summary.tsv
| | |____metc
| | | |____final_annotation_summary.tsv
| |____genbank
| | |____random_4000_gb_clean.1k.taxonomy.tsv
| | |____gb_clean_an1_virus_summary.tsv
| | |____random_4000_gb_clean.1k.fasta