Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short‐read data
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 Illumi...
Gespeichert in:
| Veröffentlicht in: | Molecular ecology resources 2024-05, Vol.24 (4), p.e13933-n/a |
|---|---|
| Hauptverfasser: | , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | n/a |
|---|---|
| container_issue | 4 |
| container_start_page | e13933 |
| container_title | Molecular ecology resources |
| container_volume | 24 |
| creator | Perry, Annabel Eddelbuettel, Dirk Rosenthal, Gil Blackmon, Heath |
| description | 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. |
| doi_str_mv | 10.1111/1755-0998.13933 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2921118564</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>3031562351</sourcerecordid><originalsourceid>FETCH-LOGICAL-c3663-f1e6f9750bc97bd231dd50b0b27aa3c6813dee3ad562c82e0eecb3a2fec741853</originalsourceid><addsrcrecordid>eNqFkbtOwzAUhi0E4lKY2ZAlFpZSO24uZqvKVSoFIZDYLMc5aQNJHOwElI1H4Bl5EhwCHVjw4tt3fvv8P0L7lBxTN0Y09P0h4Tw6powztoa2Vyfrq3X0uIV2rH0iJCA8HG-iLRZ5nLMw2kavtzrP2xM8KfEdrqR6lgvAqTZ4AaWu2yorF7jIlNFW1pDnWQ0WyzLBCdSg6u52mS2WeYsrnbeFNtUyU_h0PsGFNM9gLE6NLrBdalN_vn8YkK5U1nIXbaQyt7D3Mw_Qw_nZ_fRyOLu5uJpOZkPFgoANUwpBykOfxIqHceIxmiRuQ2IvlJKpIKIsAWAy8QNPRR4QABUz6aWgwjGNfDZAR71uZfRLA7YWRWaVa0SWoBsrPO45GyM_GDv08A_6pBtTut8JRhh1LzCfOmrUU50l1kAqKpO5XltBiegiEZ3pogtAfEfiKg5-dJu4gGTF_2bgAL8H3rIc2v_0xPXZvBf-AmX8l_w</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>3031562351</pqid></control><display><type>article</type><title>Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short‐read data</title><source>MEDLINE</source><source>Wiley Online Library All Journals</source><creator>Perry, Annabel ; Eddelbuettel, Dirk ; Rosenthal, Gil ; Blackmon, Heath</creator><creatorcontrib>Perry, Annabel ; Eddelbuettel, Dirk ; Rosenthal, Gil ; Blackmon, Heath</creatorcontrib><description>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.</description><identifier>ISSN: 1755-098X</identifier><identifier>EISSN: 1755-0998</identifier><identifier>DOI: 10.1111/1755-0998.13933</identifier><identifier>PMID: 38299378</identifier><language>eng</language><publisher>England: Wiley Subscription Services, Inc</publisher><subject>conservation genetics ; Diploids ; ecological genetics ; Genetic Markers ; Genome ; Genomes ; Genotype ; Genotypes ; Genotyping ; microsatellite ; Microsatellite Repeats ; Microsatellites ; Natural populations ; Polymorphism, Single Nucleotide ; population genetics–empirical ; Population studies ; Single-nucleotide polymorphism ; Source code</subject><ispartof>Molecular ecology resources, 2024-05, Vol.24 (4), p.e13933-n/a</ispartof><rights>2024 The Authors. published by John Wiley & Sons Ltd.</rights><rights>2024 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.</rights><rights>2024. This article is published under http://creativecommons.org/licenses/by-nc/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c3663-f1e6f9750bc97bd231dd50b0b27aa3c6813dee3ad562c82e0eecb3a2fec741853</cites><orcidid>0000-0002-5433-4036</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2F1755-0998.13933$$EPDF$$P50$$Gwiley$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2F1755-0998.13933$$EHTML$$P50$$Gwiley$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,1416,27922,27923,45572,45573</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38299378$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Perry, Annabel</creatorcontrib><creatorcontrib>Eddelbuettel, Dirk</creatorcontrib><creatorcontrib>Rosenthal, Gil</creatorcontrib><creatorcontrib>Blackmon, Heath</creatorcontrib><title>Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short‐read data</title><title>Molecular ecology resources</title><addtitle>Mol Ecol Resour</addtitle><description>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.</description><subject>conservation genetics</subject><subject>Diploids</subject><subject>ecological genetics</subject><subject>Genetic Markers</subject><subject>Genome</subject><subject>Genomes</subject><subject>Genotype</subject><subject>Genotypes</subject><subject>Genotyping</subject><subject>microsatellite</subject><subject>Microsatellite Repeats</subject><subject>Microsatellites</subject><subject>Natural populations</subject><subject>Polymorphism, Single Nucleotide</subject><subject>population genetics–empirical</subject><subject>Population studies</subject><subject>Single-nucleotide polymorphism</subject><subject>Source code</subject><issn>1755-098X</issn><issn>1755-0998</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>WIN</sourceid><sourceid>EIF</sourceid><recordid>eNqFkbtOwzAUhi0E4lKY2ZAlFpZSO24uZqvKVSoFIZDYLMc5aQNJHOwElI1H4Bl5EhwCHVjw4tt3fvv8P0L7lBxTN0Y09P0h4Tw6powztoa2Vyfrq3X0uIV2rH0iJCA8HG-iLRZ5nLMw2kavtzrP2xM8KfEdrqR6lgvAqTZ4AaWu2yorF7jIlNFW1pDnWQ0WyzLBCdSg6u52mS2WeYsrnbeFNtUyU_h0PsGFNM9gLE6NLrBdalN_vn8YkK5U1nIXbaQyt7D3Mw_Qw_nZ_fRyOLu5uJpOZkPFgoANUwpBykOfxIqHceIxmiRuQ2IvlJKpIKIsAWAy8QNPRR4QABUz6aWgwjGNfDZAR71uZfRLA7YWRWaVa0SWoBsrPO45GyM_GDv08A_6pBtTut8JRhh1LzCfOmrUU50l1kAqKpO5XltBiegiEZ3pogtAfEfiKg5-dJu4gGTF_2bgAL8H3rIc2v_0xPXZvBf-AmX8l_w</recordid><startdate>202405</startdate><enddate>202405</enddate><creator>Perry, Annabel</creator><creator>Eddelbuettel, Dirk</creator><creator>Rosenthal, Gil</creator><creator>Blackmon, Heath</creator><general>Wiley Subscription Services, Inc</general><scope>24P</scope><scope>WIN</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7SN</scope><scope>7SS</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-5433-4036</orcidid></search><sort><creationdate>202405</creationdate><title>Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short‐read data</title><author>Perry, Annabel ; Eddelbuettel, Dirk ; Rosenthal, Gil ; Blackmon, Heath</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3663-f1e6f9750bc97bd231dd50b0b27aa3c6813dee3ad562c82e0eecb3a2fec741853</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>conservation genetics</topic><topic>Diploids</topic><topic>ecological genetics</topic><topic>Genetic Markers</topic><topic>Genome</topic><topic>Genomes</topic><topic>Genotype</topic><topic>Genotypes</topic><topic>Genotyping</topic><topic>microsatellite</topic><topic>Microsatellite Repeats</topic><topic>Microsatellites</topic><topic>Natural populations</topic><topic>Polymorphism, Single Nucleotide</topic><topic>population genetics–empirical</topic><topic>Population studies</topic><topic>Single-nucleotide polymorphism</topic><topic>Source code</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Perry, Annabel</creatorcontrib><creatorcontrib>Eddelbuettel, Dirk</creatorcontrib><creatorcontrib>Rosenthal, Gil</creatorcontrib><creatorcontrib>Blackmon, Heath</creatorcontrib><collection>Wiley-Blackwell Open Access Titles</collection><collection>Wiley Free Content</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Molecular ecology resources</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Perry, Annabel</au><au>Eddelbuettel, Dirk</au><au>Rosenthal, Gil</au><au>Blackmon, Heath</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short‐read data</atitle><jtitle>Molecular ecology resources</jtitle><addtitle>Mol Ecol Resour</addtitle><date>2024-05</date><risdate>2024</risdate><volume>24</volume><issue>4</issue><spage>e13933</spage><epage>n/a</epage><pages>e13933-n/a</pages><issn>1755-098X</issn><eissn>1755-0998</eissn><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.</abstract><cop>England</cop><pub>Wiley Subscription Services, Inc</pub><pmid>38299378</pmid><doi>10.1111/1755-0998.13933</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0002-5433-4036</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1755-098X |
| ispartof | Molecular ecology resources, 2024-05, Vol.24 (4), p.e13933-n/a |
| issn | 1755-098X 1755-0998 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_2921118564 |
| source | MEDLINE; Wiley Online Library All Journals |
| subjects | conservation genetics Diploids ecological genetics Genetic Markers Genome Genomes Genotype Genotypes Genotyping microsatellite Microsatellite Repeats Microsatellites Natural populations Polymorphism, Single Nucleotide population genetics–empirical Population studies Single-nucleotide polymorphism Source code |
| title | Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short‐read data |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-09T16%3A53%3A59IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Polly:%20An%20R%20package%20for%20genotyping%20microsatellites%20and%20detecting%20highly%20polymorphic%20DNA%20markers%20from%20short%E2%80%90read%20data&rft.jtitle=Molecular%20ecology%20resources&rft.au=Perry,%20Annabel&rft.date=2024-05&rft.volume=24&rft.issue=4&rft.spage=e13933&rft.epage=n/a&rft.pages=e13933-n/a&rft.issn=1755-098X&rft.eissn=1755-0998&rft_id=info:doi/10.1111/1755-0998.13933&rft_dat=%3Cproquest_cross%3E3031562351%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=3031562351&rft_id=info:pmid/38299378&rfr_iscdi=true |