Erik Garrison, Andrea Guarracino, Simon Heumos, Flavia Villani, Zhigui Bao, Lorenzo Tattini, Jörg Hagmann, Sebastian Vorbrugg, Santiago Marco-Sola, Christian Kubica, David G Ashbrook, Kaisa Thorell, Rachel L Rusholme-Pilcher, Gianni Liti, Emilio Rudbeck, Sven Nahnsen, Zuyu Yang, Moses Njagi Mwaniki, Franklin L Nobrega, Yi Wu, Hao Chen, Joep de Ligt, Peter H Sudmant, Nicole Soranzo, Vincenza Colonna, Robert W Williams, Pjotr Prins
{"title":"构建泛基因组图谱","authors":"Erik Garrison, Andrea Guarracino, Simon Heumos, Flavia Villani, Zhigui Bao, Lorenzo Tattini, Jörg Hagmann, Sebastian Vorbrugg, Santiago Marco-Sola, Christian Kubica, David G Ashbrook, Kaisa Thorell, Rachel L Rusholme-Pilcher, Gianni Liti, Emilio Rudbeck, Sven Nahnsen, Zuyu Yang, Moses Njagi Mwaniki, Franklin L Nobrega, Yi Wu, Hao Chen, Joep de Ligt, Peter H Sudmant, Nicole Soranzo, Vincenza Colonna, Robert W Williams, Pjotr Prins","doi":"10.1101/2023.04.05.535718","DOIUrl":null,"url":null,"abstract":"<p><p>Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder (PGGB), a pipeline for constructing pangenome graphs without bias or exclusion. PGGB uses all-to-all alignments to build a variation graph in which we can identify variation, measure conservation, detect recombination events, and infer phylogenetic relationships.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10104075/pdf/","citationCount":"0","resultStr":"{\"title\":\"Building pangenome graphs.\",\"authors\":\"Erik Garrison, Andrea Guarracino, Simon Heumos, Flavia Villani, Zhigui Bao, Lorenzo Tattini, Jörg Hagmann, Sebastian Vorbrugg, Santiago Marco-Sola, Christian Kubica, David G Ashbrook, Kaisa Thorell, Rachel L Rusholme-Pilcher, Gianni Liti, Emilio Rudbeck, Sven Nahnsen, Zuyu Yang, Moses Njagi Mwaniki, Franklin L Nobrega, Yi Wu, Hao Chen, Joep de Ligt, Peter H Sudmant, Nicole Soranzo, Vincenza Colonna, Robert W Williams, Pjotr Prins\",\"doi\":\"10.1101/2023.04.05.535718\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder (PGGB), a pipeline for constructing pangenome graphs without bias or exclusion. PGGB uses all-to-all alignments to build a variation graph in which we can identify variation, measure conservation, detect recombination events, and infer phylogenetic relationships.</p>\",\"PeriodicalId\":72407,\"journal\":{\"name\":\"bioRxiv : the preprint server for biology\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-10-02\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10104075/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"bioRxiv : the preprint server for biology\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1101/2023.04.05.535718\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"bioRxiv : the preprint server for biology","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1101/2023.04.05.535718","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder (PGGB), a pipeline for constructing pangenome graphs without bias or exclusion. PGGB uses all-to-all alignments to build a variation graph in which we can identify variation, measure conservation, detect recombination events, and infer phylogenetic relationships.
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