gmRAD: an integrated SNP calling pipeline for genetic mapping with RADseq across a hybrid population.
Identifieur interne : 000B93 ( Main/Exploration ); précédent : 000B92; suivant : 000B94gmRAD: an integrated SNP calling pipeline for genetic mapping with RADseq across a hybrid population.
Auteurs : Dan Yao [République populaire de Chine] ; Hainan Wu [République populaire de Chine] ; Yuhua Chen [République populaire de Chine] ; Wenguo Yang [République populaire de Chine] ; Hua Gao [République populaire de Chine] ; Chunfa Tong [République populaire de Chine]Source :
- Briefings in bioinformatics [ 1477-4054 ] ; 2018.
Abstract
Restriction site-associated DNA sequencing (RADseq) is a powerful technology that has been extensively applied in population genetics, phylogenetics and genetic mapping. Although many software packages are available for ecological and evolutionary studies, a few effective tools are available for extracting genotype data with RADseq for genetic mapping, a prerequisite for quantitative trait locus mapping, comparative genomics and genome scaffold assembly. Here, we present an integrated pipeline called gmRAD for generating single nucleotide polymorphism (SNP) genotypes from RADseq data, de novo, across a genetic mapping population derived by crossing two parents. As an analytical strategy, the software takes five steps to implement the whole algorithms, including clustering the first (forward) reads of each parent, building two parental references, generating parental SNP catalogs, calling SNP genotypes across all individuals and filtering the genotype data for genetic linkage mapping. All the steps can be completed with a simple command line, but they can be also performed optionally if prerequisite files are available. To validate its application, we also performed a real data analysis with RADseq data from an F1 hybrid population derived by crossing Populus deltoides and Populus simonii. The software gmRAD is freely available at https://github.com/tongchf/gmRAD.
DOI: 10.1093/bib/bby114
PubMed: 30445432
Affiliations:
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Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Tong, Chunfa" sort="Tong, Chunfa" uniqKey="Tong C" first="Chunfa" last="Tong">Chunfa Tong</name><affiliation wicri:level="1"><nlm:affiliation>Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author></analytic><series><title level="j">Briefings in bioinformatics</title><idno type="eISSN">1477-4054</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Restriction site-associated DNA sequencing (RADseq) is a powerful technology that has been extensively applied in population genetics, phylogenetics and genetic mapping. Although many software packages are available for ecological and evolutionary studies, a few effective tools are available for extracting genotype data with RADseq for genetic mapping, a prerequisite for quantitative trait locus mapping, comparative genomics and genome scaffold assembly. Here, we present an integrated pipeline called gmRAD for generating single nucleotide polymorphism (SNP) genotypes from RADseq data, de novo, across a genetic mapping population derived by crossing two parents. As an analytical strategy, the software takes five steps to implement the whole algorithms, including clustering the first (forward) reads of each parent, building two parental references, generating parental SNP catalogs, calling SNP genotypes across all individuals and filtering the genotype data for genetic linkage mapping. All the steps can be completed with a simple command line, but they can be also performed optionally if prerequisite files are available. To validate its application, we also performed a real data analysis with RADseq data from an F1 hybrid population derived by crossing Populus deltoides and Populus simonii. The software gmRAD is freely available at https://github.com/tongchf/gmRAD.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">30445432</PMID><DateRevised><Year>2020</Year><Month>08</Month><Day>17</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1477-4054</ISSN><JournalIssue CitedMedium="Internet"><PubDate><Year>2018</Year><Month>11</Month><Day>14</Day></PubDate></JournalIssue><Title>Briefings in bioinformatics</Title><ISOAbbreviation>Brief Bioinform</ISOAbbreviation></Journal><ArticleTitle>gmRAD: an integrated SNP calling pipeline for genetic mapping with RADseq across a hybrid population.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1093/bib/bby114</ELocationID><Abstract><AbstractText>Restriction site-associated DNA sequencing (RADseq) is a powerful technology that has been extensively applied in population genetics, phylogenetics and genetic mapping. Although many software packages are available for ecological and evolutionary studies, a few effective tools are available for extracting genotype data with RADseq for genetic mapping, a prerequisite for quantitative trait locus mapping, comparative genomics and genome scaffold assembly. Here, we present an integrated pipeline called gmRAD for generating single nucleotide polymorphism (SNP) genotypes from RADseq data, de novo, across a genetic mapping population derived by crossing two parents. As an analytical strategy, the software takes five steps to implement the whole algorithms, including clustering the first (forward) reads of each parent, building two parental references, generating parental SNP catalogs, calling SNP genotypes across all individuals and filtering the genotype data for genetic linkage mapping. All the steps can be completed with a simple command line, but they can be also performed optionally if prerequisite files are available. To validate its application, we also performed a real data analysis with RADseq data from an F1 hybrid population derived by crossing Populus deltoides and Populus simonii. The software gmRAD is freely available at https://github.com/tongchf/gmRAD.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yao</LastName><ForeName>Dan</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Hainan</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Yuhua</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Wenguo</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gao</LastName><ForeName>Hua</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tong</LastName><ForeName>Chunfa</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Southern Modern Forestry Collaborative Innovation Center, College of Forestry, Nanjing Forestry University, Nanjing, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>11</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Brief Bioinform</MedlineTA><NlmUniqueID>100912837</NlmUniqueID><ISSNLinking>1467-5463</ISSNLinking></MedlineJournalInfo><CommentsCorrectionsList><CommentsCorrections RefType="ErratumIn"><RefSource>Brief Bioinform. 2020 Mar 23;21(2):752</RefSource><PMID Version="1">30649178</PMID></CommentsCorrections></CommentsCorrectionsList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>08</Month><Day>01</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>10</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>11</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>11</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>11</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>aheadofprint</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30445432</ArticleId><ArticleId IdType="pii">5181553</ArticleId><ArticleId IdType="doi">10.1093/bib/bby114</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Yao, Dan" sort="Yao, Dan" uniqKey="Yao D" first="Dan" last="Yao">Dan Yao</name></noRegion><name sortKey="Chen, Yuhua" sort="Chen, Yuhua" uniqKey="Chen Y" first="Yuhua" last="Chen">Yuhua Chen</name><name sortKey="Gao, Hua" sort="Gao, Hua" uniqKey="Gao H" first="Hua" last="Gao">Hua Gao</name><name sortKey="Tong, Chunfa" sort="Tong, Chunfa" uniqKey="Tong C" first="Chunfa" last="Tong">Chunfa Tong</name><name sortKey="Wu, Hainan" sort="Wu, Hainan" uniqKey="Wu H" first="Hainan" last="Wu">Hainan Wu</name><name sortKey="Yang, Wenguo" sort="Yang, Wenguo" uniqKey="Yang W" first="Wenguo" last="Yang">Wenguo Yang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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