{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T09:02:58Z","timestamp":1789635778014,"version":"4.0.0"},"reference-count":53,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T00:00:00Z","timestamp":1789603200000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The Spanish Ministry of Science and Innovation grants","award":["PID2020-120115GB-100"],"award-info":[{"award-number":["PID2020-120115GB-100"]}]},{"name":"The Spanish Ministry of Science and Innovation grants","award":["PID2023-152577NB-I00"],"award-info":[{"award-number":["PID2023-152577NB-I00"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>\n                    Multiplexed amplicon sequencing has become an important tool in phylogenetics and conservation genetics. Amplicon sequencing reads need to be processed to get final haplotypes. The bioinformatics involved is often limiting for embarking on these kind of projects and there are few tools designed to handle this type of data.\n                    <jats:italic>tidyGenR<\/jats:italic>\n                    is an R package for reproducible multilocus amplicon genotyping workflows from sequencing reads. It provides a modular workflow that starts by demultiplexing loci, variant determination with\n                    <jats:italic>DADA2<\/jats:italic>\n                    , and ends with genotyping. Input data can be raw single-end or paired-end FASTQ reads and the main outputs are haplotypes in tidy tables. Results can also be exported as FASTA files. We successfully tested\n                    <jats:italic>tidyGenR<\/jats:italic>\n                    on amplicon libraries of 27 loci from a population genetics study in a rodent. The results from\n                    <jats:italic>tidyGenR<\/jats:italic>\n                    were reliable and robust across a wide range of read depths. In addition,\n                    <jats:italic>tidyGenR<\/jats:italic>\n                    offers greater flexibility and interoperability.\n                  <\/jats:p>","DOI":"10.7717\/peerj.21726","type":"journal-article","created":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T08:20:19Z","timestamp":1789633219000},"page":"e21726","source":"Crossref","is-referenced-by-count":0,"title":["tidyGenR: tidy multilocus amplicon genotypes in R"],"prefix":"10.7717","volume":"14","author":[{"given":"Miguel","family":"Camacho-Sanchez","sequence":"first","affiliation":[{"name":"Conservation and Evolutionary Genetics Group, Estaci\u00f3n Biol\u00f3gica de Do\u00f1ana, Consejo Superior de Investigaciones Cient\u00edficas, Sevilla, Spain"},{"name":"Institute of Organismic and Molecular Evolution (iomE), Anthropologie (iomE), Johannes-Gutenberg Universit\u00e4t Mainz, Mainz, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer 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