{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:42:24Z","timestamp":1753875744750,"version":"3.41.2"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2023,4,17]],"date-time":"2023-04-17T00:00:00Z","timestamp":1681689600000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory","award":["Guangzhou"],"award-info":[{"award-number":["Guangzhou"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,4,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Primer design is a routine practice for modern molecular biology labs. Bioinformatics tools like primer3 and primer-blast have standardized the primer design for a specific region. However, large-scale primer design, especially for genome-wide screening, is still a labor-intensive job for most wet-lab researchers using these pipelines.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present the primerdiffer pipeline, which can be used to batch design primers that differentiate haplotypes on a large scale with precise false priming checking. This command-line interface (CLI) pipeline includes greedy primer search, local and global in silico PCR-based false priming checking, and automated best primer selection. The local CLI application provides flexibility to design primers with the user\u2019s own genome sequences and specific parameters. Some species-specific primers designed to genotype the hybrid introgression strains from Caenorhabditis briggsae and Caenorhabditis nigoni have been validated using single-worm PCR. This pipeline provides the first CLI-based large-scale primer design tool to differentiate haplotypes in any targeted region.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The open-source python modules are available at github (https:\/\/github.com\/runsheng\/primerdiffer, https:\/\/github.com\/runsheng\/primervcf) and Python package index (https:\/\/pypi.org\/project\/primerdiffer\/, https:\/\/pypi.org\/project\/primervcf\/).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad188","type":"journal-article","created":{"date-parts":[[2023,4,17]],"date-time":"2023-04-17T14:24:24Z","timestamp":1681741464000},"source":"Crossref","is-referenced-by-count":2,"title":["Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping"],"prefix":"10.1093","volume":"39","author":[{"given":"Xiaoliang","family":"Ren","sequence":"first","affiliation":[{"name":"Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences , Qingdao 266071, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanwen","family":"Shao","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yiwen","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ying","family":"Ni","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences and Tung Biomedical Sciences Centre, City University of Hong Kong , Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu","family":"Bi","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1563-1844","authenticated-orcid":false,"given":"Runsheng","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong , Hong Kong, China"},{"name":"Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) , Guangzhou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,4,17]]},"reference":[{"key":"2023042123012389700_btad188-B1","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1186\/1471-2105-9-465","article-title":"QuantPrime\u2014a flexible tool for reliable high-throughput primer design for quantitative PCR","volume":"9","author":"Arvidsson","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023042123012389700_btad188-B2","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/1745-6150-7-12","article-title":"Domain enhanced lookup time accelerated BLAST","volume":"7","author":"Boratyn","year":"2012","journal-title":"Biol Direct"},{"key":"2023042123012389700_btad188-B3","doi-asserted-by":"crossref","first-page":"W614","DOI":"10.1093\/nar\/gkz323","article-title":"MRPrimerW2: an enhanced tool for rapid design of valid high-quality primers with multiple search modes for qPCR experiments","volume":"47","author":"Jeon","year":"2019","journal-title":"Nucleic Acids Res"},{"author":"Li","key":"2023042123012389700_btad188-B4"},{"key":"2023042123012389700_btad188-B5","doi-asserted-by":"crossref","first-page":"2038","DOI":"10.1093\/bioinformatics\/btv069","article-title":"PolyMarker: a fast polyploid primer design pipeline","volume":"31","author":"Ramirez-Gonzalez","year":"2015","journal-title":"Bioinformatics"},{"key":"2023042123012389700_btad188-B6","doi-asserted-by":"crossref","first-page":"e115","DOI":"10.1093\/nar\/gks596","article-title":"Primer3\u2014new capabilities and interfaces","volume":"40","author":"Untergasser","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023042123012389700_btad188-B7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-13-S6-S1","article-title":"Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction","volume":"13","author":"Ye","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023042123012389700_btad188-B8","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1186\/1471-2105-9-253","article-title":"BatchPrimer3: a high throughput web application for PCR and sequencing primer design","volume":"9","author":"You","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023042123012389700_btad188-B9","doi-asserted-by":"crossref","first-page":"e82138","DOI":"10.1371\/journal.pone.0082138","article-title":"SSW library: an SIMD Smith-Waterman C\/C++ library for use in genomic applications","volume":"8","author":"Zhao","year":"2013","journal-title":"PLoS One"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad188\/49989157\/btad188.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/4\/btad188\/50062624\/btad188.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/4\/btad188\/50062624\/btad188.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,21]],"date-time":"2023-04-21T23:02:05Z","timestamp":1682118125000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad188\/7126407"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2023,4,1]]},"references-count":9,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2023,4,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad188","relation":{},"ISSN":["1367-4811"],"issn-type":[{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2023,4,1]]},"published":{"date-parts":[[2023,4,1]]},"article-number":"btad188"}}