Evidence map›Paper›PMID 38299378›Full record

ArticleMolecular ecology resources2024

Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short-read data.

Annabel Perry, Dirk Eddelbuettel, Gil Rosenthal, Heath Blackmon

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular ecology resources, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

4 authors.

Annabel PerryDepartment of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.
Dirk EddelbuettelDepartment of Statistics, University of Illinois Urbana-Champagne, Urbana, Illinois, USA.
Gil RosenthalDepartment of Biology, Texas A&M University, College Station, Texas, USA.
Heath BlackmonDepartment of Biology, Texas A&M University, College Station, Texas, USA.ORCID https://orcid.org/0000-0002-5433-4036

Funding

Integrating theory, genomics, and comparative approaches to break barriers to the understanding of genome structure and sex chromosome evolution.R35GM138098 · NIGMS · TEXAS A&M UNIVERSITY · PI BLACKMON, HEATH · 2020 to 2024
$1.8M
NIGMS NIH HHS R35 GM138098NIGMS NIH HHS R35GM138098
6 · The paper itself

Abstract

Highly polymorphic markers, such as microsatellites, are invaluable for the study of natural populations. However, contemporary methods for genotyping highly polymorphic variants have serious drawbacks that impede their efficiency. We created Polly, an R package with C++ source code that uses Illumina short-read data to genotype microsatellites, detect highly polymorphic variants and identify clusters of highly polymorphic SNPs, indels and microsatellites. We tested Polly on short-read data from Xiphophorus birchmanni (Teleostei: Poeciliidae) and Arabidopsis thaliana, finding it to be efficient and accurate both for microsatellite genotyping and polymorphic marker detection. This program can be applied to any diploid population for which there exists short-read data and at least one scaffolded reference genome.

Indexed as

GenomePolymorphism, Single NucleotideGenetic MarkersGenotypeMicrosatellite RepeatsGenetic Markersconservation geneticsecological geneticsgenotypemicrosatellitepopulation genetics–empirical

Identifiers

PMID38299378
PMCPMC10994724

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Registered trials

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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.