Evidence map›Paper›PMID 42316291›Full record

ArticleGenome biology2026

Aardvark: sifting through differences in a mound of variants.

James M Holt, Christopher T Saunders, Egor Dolzhenko, Peter Krusche, Nathan D Olson, Justin M Zook, Michael A Eberle, Zev Kronenberg

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. A complete human pancreatic cancer genome.bioRxiv : the preprint server for biology · 2026
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

James M HoltPacBio, 1305 O'Brien Drive, Menlo Park, 94025, CA, USA. mholt@pacificbiosciences.com.
Christopher T SaundersPacBio, 1305 O'Brien Drive, Menlo Park, 94025, CA, USA.
Egor DolzhenkoPacBio, 1305 O'Brien Drive, Menlo Park, 94025, CA, USA.
Peter KruscheNovartis Pharma AG, Basel, CH-4056, Switzerland.
Nathan D OlsonMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, 20899, MD, USA.
Justin M ZookMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, 20899, MD, USA.
Michael A Eberle *PacBio, 1305 O'Brien Drive, Menlo Park, 94025, CA, USA.
Zev Kronenberg *PacBio, 1305 O'Brien Drive, Menlo Park, 94025, CA, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Variant benchmarking is critical in assessing the accuracy of genomic secondary pipelines. However, traditional benchmarking tools that require exact genotype matches inject biases from variant representation and are ill-suited for tandem repeat or structural variation. We describe Aardvark, a variant benchmarking tool that introduces the basepair score to directly compare haplotype sequences, reducing representation biases while allowing for partial credit scoring. The tool also includes the traditional genotype score and supports separate or joint benchmarking of small variants, tandem repeats, and structural variants (<10 kb). Aardvark accepts standard inputs, runs

Indexed as

Genetic VariationGenomicsSoftwareBenchmarkingHaplotypesHumansTandem Repeat SequencesStructural variantsTandem repeatsVariant benchmarkingVariant calling

Identifiers

PMID42316291
PMCPMC13520500

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.