Response to: "best practices when benchmarking CATCH for the design of genome enrichment probes".

Jarno N Alanko, Ilya B Slizovskiy, Daniel Lokshtanov, Travis Gagie, Noelle R Noyes, Christina Boucher

Abstract read

In one paragraph

Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

6 authors.

Jarno N AlankoDepartment of Computer Science, University of Helsinki, 00014 Helsinki, Finland.ORCID 0000-0002-8003-9225

Ilya B SlizovskiyCollege of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, United States.ORCID 0000-0002-0758-5510

Daniel LokshtanovDepartment of Computer Science, University of California, Santa Barbara, CA 93106, United States.

Travis GagieFaculty of Computer Science, Dalhousie University, Halifax, NS, B3H 4R2, Canada.ORCID 0000-0003-3689-327X

Noelle R NoyesDepartment of Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108, United States.ORCID 0000-0001-6149-1008

Christina BoucherDepartment of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, United States.ORCID 0000-0001-9509-9725

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

We clarify the design principles and evaluation choices underlying Syotti, a robust and scalable probe-design tool developed to support large, heterogeneous bacterial datasets with minimal parameter tuning. We highlight Syotti's ability to perform simultaneous large-scale designs and its effectiveness as a reliable alternative when existing tools such as CATCH are not well suited to the problem setting.

Indexed as

Genome, BacterialGenomicsSoftwareBenchmarking

Identifiers

PMID41776823

DOI10.1093/bioinformatics/btag100

PMCPMC12996868

What OpenQuestion holds

Textmetadata

LicenceCC BY

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.