{ "source_dataset": "CAMI II human-associated short-read gold-standard assemblies and simulated reads", "source_doi": "10.4126/FRL01-006425518", "selection": "Prepare tiny real CAMI inputs; requires minimap2, not MetaPathways or Pathway Tools.\n\nSelect three abundant genomes per sample, retain up to 50 kb of one contig each,\nthen retain intact original read pairs with a primary MAPQ >=20 alignment to\nthose regions from the first 250,000 pairs. This is deliberately coverage-biased\ninterface test data, never an abundance or accuracy benchmark.\n", "minimap2_version": "2.31-r1302", "samples": [ { "sample_id": "Urogenital_22", "source_assembly": "/data/home/ryan/data/mock_2022/MetaGs/CAMI_II_Urogenital/short_read/2017.12.04_18.56.22_sample_22/contigs/anonymous_gsa.fasta", "source_reads": "/data/home/ryan/data/mock_2022/MetaGs/CAMI_II_Urogenital/short_read/2017.12.04_18.56.22_sample_22/reads/anonymous_reads.fq.gz", "source_mapping": "/data/home/ryan/data/mock_2022/MetaGs/CAMI_II_Urogenital/short_read/2017.12.04_18.56.22_sample_22/contigs/gsa_mapping.tsv", "scanned_pairs": 250000, "retained_pairs": 3000, "assembly_bases": 150000, "regions": [ { "#anonymous_contig_id": "S22C5358", "genome_id": "OTU_97.19349.0", "tax_id": "1578", "contig_id": "CP002341.1", "number_reads": "2550346", "start_position": "2", "end_position": "2125751", "retained_contig_start_1based": 1, "retained_contig_end_1based": 50000, "aligned_pairs": 1460 }, { "#anonymous_contig_id": "S22C8829", "genome_id": "OTU_97.578.0", "tax_id": "1763", "contig_id": "CP018363.1", "number_reads": "5712090", "start_position": "1", "end_position": "5626623", "retained_contig_start_1based": 1, "retained_contig_end_1based": 50000, "aligned_pairs": 299 }, { "#anonymous_contig_id": "S22C9504", "genome_id": "OTU_97.39620.0", "tax_id": "1578", "contig_id": "CP011403.1", "number_reads": "10184206", "start_position": "1", "end_position": "1751564", "retained_contig_start_1based": 1, "retained_contig_end_1based": 50000, "aligned_pairs": 1241 } ] }, { "sample_id": "Gastrointestinal_5", "source_assembly": "/data/home/ryan/data/mock_2022/MetaGs/CAMI_II_Gastrointestinal/short_read/2017.12.04_18.45.54_sample_5/contigs/anonymous_gsa.fasta", "source_reads": "/data/home/ryan/data/mock_2022/MetaGs/CAMI_II_Gastrointestinal/short_read/2017.12.04_18.45.54_sample_5/reads/anonymous_reads.fq.gz", "source_mapping": "/data/home/ryan/data/mock_2022/MetaGs/CAMI_II_Gastrointestinal/short_read/2017.12.04_18.45.54_sample_5/contigs/gsa_mapping.tsv", "scanned_pairs": 250000, "retained_pairs": 2326, "assembly_bases": 150000, "regions": [ { "#anonymous_contig_id": "S5C2519", "genome_id": "OTU_97.1154.0", "tax_id": "506", "contig_id": "HE965803.1", "number_reads": "5485844", "start_position": "2", "end_position": "4887378", "retained_contig_start_1based": 1, "retained_contig_end_1based": 50000, "aligned_pairs": 951 }, { "#anonymous_contig_id": "S5C5928", "genome_id": "OTU_97.68.0", "tax_id": "841", "contig_id": "CP003040.1", "number_reads": "3359972", "start_position": "6", "end_position": "3592124", "retained_contig_start_1based": 1, "retained_contig_end_1based": 50000, "aligned_pairs": 731 }, { "#anonymous_contig_id": "S5C5950", "genome_id": "OTU_97.44483.0", "tax_id": "541000", "contig_id": "CP004044.1", "number_reads": "1411892", "start_position": "2", "end_position": "905459", "retained_contig_start_1based": 1, "retained_contig_end_1based": 50000, "aligned_pairs": 644 } ] }, { "sample_id": "Skin_28", "source_assembly": "/data/home/ryan/data/mock_2022/MetaGs/CAMI_II_Skin/short_read/2017.12.04_18.56.22_sample_28/contigs/anonymous_gsa.fasta", "source_reads": "/data/home/ryan/data/mock_2022/MetaGs/CAMI_II_Skin/short_read/2017.12.04_18.56.22_sample_28/reads/anonymous_reads.fq.gz", "source_mapping": "/data/home/ryan/data/mock_2022/MetaGs/CAMI_II_Skin/short_read/2017.12.04_18.56.22_sample_28/contigs/gsa_mapping.tsv", "scanned_pairs": 250000, "retained_pairs": 3000, "assembly_bases": 150000, "regions": [ { "#anonymous_contig_id": "S28C1233", "genome_id": "OTU_97.44585.0", "tax_id": "1279", "contig_id": "BA000018.3", "number_reads": "5213080", "start_position": "1", "end_position": "2814815", "retained_contig_start_1based": 1, "retained_contig_end_1based": 50000, "aligned_pairs": 764 }, { "#anonymous_contig_id": "S28C1662", "genome_id": "OTU_97.34494.0", "tax_id": 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