SRR28267218 · Gut microbiome

Metagenome or environmental sample from gut metagenome

complete

Gut analysis is paused. Unfinished samples are not negative results. This is a mixed-host collection, not a curated human-only cohort.

Open interactive sample report

Taxonomic abundances

Saved public metadata

{
  "run_accession": "SRR28267218",
  "study_accession": "PRJNA1082425",
  "sample_accession": "SAMN40210563",
  "instrument_platform": "OXFORD_NANOPORE",
  "instrument_model": "GridION",
  "library_strategy": "AMPLICON",
  "library_source": "GENOMIC",
  "library_selection": "PCR",
  "read_count": "113855",
  "base_count": "186007186",
  "fastq_bytes": "156099354",
  "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR282/018/SRR28267218/SRR28267218_1.fastq.gz",
  "sample_title": "Metagenome or environmental sample from gut metagenome",
  "scientific_name": "gut metagenome"
}

Public files

SRR28267218_1.fastq.gz

Analysis provenance

{
  "marker": "16S",
  "pipeline": "Archaions v18.8",
  "cohort": "Gut, mixed hosts; not curated as a human-only cohort",
  "execution_state": "paused_by_user",
  "sample_state": "complete",
  "read_sampling": "First available reads; not random subsampling",
  "input_sha256": "1123aaffa56732b6b61302e81802aab2ff70d2794db490b63ae8df1fc5c8ea1b",
  "length_window_bp": [
    1200,
    2000
  ],
  "median_read_length": 1640.0,
  "quality_scores": "No measured quality scores in fetched FASTA",
  "classifier_stats": {
    "marker": "16s",
    "pipeline": "v18.8",
    "gpu": "RTX-PRO-6000",
    "input_path": "volume-fastq-gz",
    "reads_in": 20000,
    "reads_skipped": 6777,
    "elapsed_seconds": 1.9264803989999564,
    "reads_submitted": 20000,
    "reads_after_filter": 20000,
    "adapter_scan": {
      "sampled": 200,
      "matched": 106,
      "fraction": 0.53,
      "adapters_found": {
        "RAP": 96,
        "BC_FLANK": 8,
        "1492R_rc": 1,
        "27F": 1
      },
      "should_trim": true
    },
    "porechop_ran": false,
    "porechop_reason": "fast-path: no adapter trimming required"
  },
  "metadata_coverage": "Saved ENA run fields only. BioSample attributes, study abstracts and file MD5s have not been fetched for this panel."
}