{
  "abstract": "Marker-gene amplicon workflows are routinely run on shared compute, yet the cores, memory and wall time they are given are chosen by convention and not by measurement. We present a protocol for measuring them, applied to the two dominant stages of a QIIME 2 16S rRNA pipeline, DADA2 denoising and Naive Bayes taxonomic classification, across nine upper-respiratory samples from a paediatric otitis media cohort. The two stages do not consume the same input: denoising reads every sequence, classification only those surviving it. Subsampling one library across a 27-fold range of sequencing depth, denoising wall time rose 14.3-fold while classification changed by 1% and its peak memory not at all (3.11 GiB). Amplicon sequence variant (ASV) richness rose 2.8-fold over that range, so this is not richness saturating: the stage is dominated by a fixed per-invocation cost. Across a body-site gradient of 5 to 70 ASVs, denoising followed read count (exponent 0.75) while classification followed neither: a 5-ASV effusion and a 70-ASV adenoid community cost 40.81 s and 40.79 s. One ASV took 36.20 s and 218 took 37.27 s, 97% fixed cost. Thread-level parallelism offered little benefit. Denoising peaked at 1.18x near 8 threads and then declined; classification was slower at every setting above one job, consuming 10.5 times the CPU at 40. Representative sequences and their taxonomic assignments were identical at 1, 4 and 40 threads, so a reduced allocation changes what the analysis costs, not what it reports. Extending the query set to 10,000 sequences located two distinct boundaries: eight jobs first beat one at roughly 5,000 queries, and fitted fixed and per-query costs become equal at 15,248. Both lie roughly two orders of magnitude above the richest single sample measured. Practically: size denoising by read count, calibrate classification once against the reference in use, request one job for classification below a few thousand sequences, and take throughput from sample-level parallelism. Protocol, data and analysis code are released with the pipeline.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Computer Science and Engineering, Sri Eshwar College of Engineering, Coimbatore, Tamil Nadu, India"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "S. Victor"
    },
    {
      "name": "S. Sadasivam"
    },
    {
      "name": "Y. S"
    },
    {
      "name": "S. R"
    },
    {
      "name": "S. A. P"
    },
    {
      "name": "G. Satheesh"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/98cmhzrew2g42.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.01.748377",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.01.748377v1.full",
  "id": "98cmhzrew2g42",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.01.748377v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "bioinformatics"
    ],
    [
      "openalex",
      "1312|Genomics and Phylogenetic Studies"
    ]
  ],
  "openalex": "W7204997165",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.01.748377v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-01",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/98cmhzrew2g42.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:23Z",
      "native_id": "10.64898/2026.09.01.748377",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.01.748377v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "Taxonomic classification cost tracks neither sequencing depth nor community richness at single-sample scale: a measured resource protocol for 16S rRNA amplicon pipelines",
  "title_text": "Taxonomic classification cost tracks neither sequencing depth nor community richness at single-sample scale: a measured resource protocol for 16S rRNA amplicon pipelines",
  "type": "preprint",
  "updated_at": "2026-10-30T12:18:23Z",
  "url": "https://research.draconitic.com/paper/98cmhzrew2g42",
  "venue": "bioRxiv",
  "versions": []
}