David Porubsky1,2, Ashley D Sanders3,4, Aaron Taudt1,5, Maria Colomé-Tatché1,5, Peter M Lansdorp1,3,6, Victor Guryev1. 1. European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands. 2. Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. 3. Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, Canada. 4. European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany. 5. Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany. 6. Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
Abstract
MOTIVATION: Strand-seq is a specialized single-cell DNA sequencing technique centered around the directionality of single-stranded DNA. Computational tools for Strand-seq analyses must capture the strand-specific information embedded in these data. RESULTS: Here we introduce breakpointR, an R/Bioconductor package specifically tailored to process and interpret single-cell strand-specific sequencing data obtained from Strand-seq. We developed breakpointR to detect local changes in strand directionality of aligned Strand-seq data, to enable fine-mapping of sister chromatid exchanges, germline inversion and to support global haplotype assembly. Given the broad spectrum of Strand-seq applications we expect breakpointR to be an important addition to currently available tools and extend the accessibility of this novel sequencing technique. AVAILABILITY AND IMPLEMENTATION: R/Bioconductor package https://bioconductor.org/packages/breakpointR. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Strand-seq is a specialized single-cell DNA sequencing technique centered around the directionality of single-stranded DNA. Computational tools for Strand-seq analyses must capture the strand-specific information embedded in these data. RESULTS: Here we introduce breakpointR, an R/Bioconductor package specifically tailored to process and interpret single-cell strand-specific sequencing data obtained from Strand-seq. We developed breakpointR to detect local changes in strand directionality of aligned Strand-seq data, to enable fine-mapping of sister chromatid exchanges, germline inversion and to support global haplotype assembly. Given the broad spectrum of Strand-seq applications we expect breakpointR to be an important addition to currently available tools and extend the accessibility of this novel sequencing technique. AVAILABILITY AND IMPLEMENTATION: R/Bioconductor package https://bioconductor.org/packages/breakpointR. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Erich D Jarvis; Giulio Formenti; Arang Rhie; Andrea Guarracino; Chentao Yang; Jonathan Wood; Alan Tracey; Francoise Thibaud-Nissen; Mitchell R Vollger; David Porubsky; Haoyu Cheng; Mobin Asri; Glennis A Logsdon; Paolo Carnevali; Mark J P Chaisson; Chen-Shan Chin; Sarah Cody; Joanna Collins; Peter Ebert; Merly Escalona; Olivier Fedrigo; Robert S Fulton; Lucinda L Fulton; Shilpa Garg; Jennifer L Gerton; Jay Ghurye; Anastasiya Granat; Richard E Green; William Harvey; Patrick Hasenfeld; Alex Hastie; Marina Haukness; Erich B Jaeger; Miten Jain; Melanie Kirsche; Mikhail Kolmogorov; Jan O Korbel; Sergey Koren; Jonas Korlach; Joyce Lee; Daofeng Li; Tina Lindsay; Julian Lucas; Feng Luo; Tobias Marschall; Matthew W Mitchell; Jennifer McDaniel; Fan Nie; Hugh E Olsen; Nathan D Olson; Trevor Pesout; Tamara Potapova; Daniela Puiu; Allison Regier; Jue Ruan; Steven L Salzberg; Ashley D Sanders; Michael C Schatz; Anthony Schmitt; Valerie A Schneider; Siddarth Selvaraj; Kishwar Shafin; Alaina Shumate; Nathan O Stitziel; Catherine Stober; James Torrance; Justin Wagner; Jianxin Wang; Aaron Wenger; Chuanle Xiao; Aleksey V Zimin; Guojie Zhang; Ting Wang; Heng Li; Erik Garrison; David Haussler; Ira Hall; Justin M Zook; Evan E Eichler; Adam M Phillippy; Benedict Paten; Kerstin Howe; Karen H Miga Journal: Nature Date: 2022-10-19 Impact factor: 69.504
Authors: David Porubsky; Wolfram Höps; Hufsah Ashraf; PingHsun Hsieh; Bernardo Rodriguez-Martin; Feyza Yilmaz; Jana Ebler; Pille Hallast; Flavia Angela Maria Maggiolini; William T Harvey; Barbara Henning; Peter A Audano; David S Gordon; Peter Ebert; Patrick Hasenfeld; Eva Benito; Qihui Zhu; Charles Lee; Francesca Antonacci; Matthias Steinrücken; Christine R Beck; Ashley D Sanders; Tobias Marschall; Evan E Eichler; Jan O Korbel Journal: Cell Date: 2022-05-06 Impact factor: 66.850
Authors: Vincent C T Hanlon; Daniel D Chan; Zeid Hamadeh; Yanni Wang; Carl-Adam Mattsson; Diana C J Spierings; Robin J N Coope; Peter M Lansdorp Journal: Cell Rep Methods Date: 2022-01-24
Authors: Peter Ebert; Peter A Audano; Qihui Zhu; Bernardo Rodriguez-Martin; Charles Lee; Jan O Korbel; Tobias Marschall; Evan E Eichler; David Porubsky; Marc Jan Bonder; Arvis Sulovari; Jana Ebler; Weichen Zhou; Rebecca Serra Mari; Feyza Yilmaz; Xuefang Zhao; PingHsun Hsieh; Joyce Lee; Sushant Kumar; Jiadong Lin; Tobias Rausch; Yu Chen; Jingwen Ren; Martin Santamarina; Wolfram Höps; Hufsah Ashraf; Nelson T Chuang; Xiaofei Yang; Katherine M Munson; Alexandra P Lewis; Susan Fairley; Luke J Tallon; Wayne E Clarke; Anna O Basile; Marta Byrska-Bishop; André Corvelo; Uday S Evani; Tsung-Yu Lu; Mark J P Chaisson; Junjie Chen; Chong Li; Harrison Brand; Aaron M Wenger; Maryam Ghareghani; William T Harvey; Benjamin Raeder; Patrick Hasenfeld; Allison A Regier; Haley J Abel; Ira M Hall; Paul Flicek; Oliver Stegle; Mark B Gerstein; Jose M C Tubio; Zepeng Mu; Yang I Li; Xinghua Shi; Alex R Hastie; Kai Ye; Zechen Chong; Ashley D Sanders; Michael C Zody; Michael E Talkowski; Ryan E Mills; Scott E Devine Journal: Science Date: 2021-02-25 Impact factor: 47.728
Authors: Sergey Nurk; Sergey Koren; Arang Rhie; Mikko Rautiainen; Andrey V Bzikadze; Alla Mikheenko; Mitchell R Vollger; Nicolas Altemose; Lev Uralsky; Ariel Gershman; Sergey Aganezov; Savannah J Hoyt; Mark Diekhans; Glennis A Logsdon; Michael Alonge; Stylianos E Antonarakis; Matthew Borchers; Gerard G Bouffard; Shelise Y Brooks; Gina V Caldas; Nae-Chyun Chen; Haoyu Cheng; Chen-Shan Chin; William Chow; Leonardo G de Lima; Philip C Dishuck; Richard Durbin; Tatiana Dvorkina; Ian T Fiddes; Giulio Formenti; Robert S Fulton; Arkarachai Fungtammasan; Erik Garrison; Patrick G S Grady; Tina A Graves-Lindsay; Ira M Hall; Nancy F Hansen; Gabrielle A Hartley; Marina Haukness; Kerstin Howe; Michael W Hunkapiller; Chirag Jain; Miten Jain; Erich D Jarvis; Peter Kerpedjiev; Melanie Kirsche; Mikhail Kolmogorov; Jonas Korlach; Milinn Kremitzki; Heng Li; Valerie V Maduro; Tobias Marschall; Ann M McCartney; Jennifer McDaniel; Danny E Miller; James C Mullikin; Eugene W Myers; Nathan D Olson; Benedict Paten; Paul Peluso; Pavel A Pevzner; David Porubsky; Tamara Potapova; Evgeny I Rogaev; Jeffrey A Rosenfeld; Steven L Salzberg; Valerie A Schneider; Fritz J Sedlazeck; Kishwar Shafin; Colin J Shew; Alaina Shumate; Ying Sims; Arian F A Smit; Daniela C Soto; Ivan Sović; Jessica M Storer; Aaron Streets; Beth A Sullivan; Françoise Thibaud-Nissen; James Torrance; Justin Wagner; Brian P Walenz; Aaron Wenger; Jonathan M D Wood; Chunlin Xiao; Stephanie M Yan; Alice C Young; Samantha Zarate; Urvashi Surti; Rajiv C McCoy; Megan Y Dennis; Ivan A Alexandrov; Jennifer L Gerton; Rachel J O'Neill; Winston Timp; Justin M Zook; Michael C Schatz; Evan E Eichler; Karen H Miga; Adam M Phillippy Journal: Science Date: 2022-03-31 Impact factor: 63.714
Authors: Glennis A Logsdon; Mitchell R Vollger; PingHsun Hsieh; Yafei Mao; Mikhail A Liskovykh; Sergey Koren; Sergey Nurk; Ludovica Mercuri; Philip C Dishuck; Arang Rhie; Leonardo G de Lima; Tatiana Dvorkina; David Porubsky; William T Harvey; Alla Mikheenko; Andrey V Bzikadze; Milinn Kremitzki; Tina A Graves-Lindsay; Chirag Jain; Kendra Hoekzema; Shwetha C Murali; Katherine M Munson; Carl Baker; Melanie Sorensen; Alexandra M Lewis; Urvashi Surti; Jennifer L Gerton; Vladimir Larionov; Mario Ventura; Karen H Miga; Adam M Phillippy; Evan E Eichler Journal: Nature Date: 2021-04-07 Impact factor: 69.504
Authors: Flavia Angela Maria Maggiolini; Ashley D Sanders; Colin James Shew; Arvis Sulovari; Yafei Mao; Marta Puig; Claudia Rita Catacchio; Maria Dellino; Donato Palmisano; Ludovica Mercuri; Miriana Bitonto; David Porubský; Mario Cáceres; Evan E Eichler; Mario Ventura; Megan Y Dennis; Jan O Korbel; Francesca Antonacci Journal: Genome Res Date: 2020-10-22 Impact factor: 9.043
Authors: David Porubsky; Ashley D Sanders; Wolfram Höps; PingHsun Hsieh; Arvis Sulovari; Ruiyang Li; Ludovica Mercuri; Melanie Sorensen; Shwetha C Murali; David Gordon; Stuart Cantsilieris; Alex A Pollen; Mario Ventura; Francesca Antonacci; Tobias Marschall; Jan O Korbel; Evan E Eichler Journal: Nat Genet Date: 2020-06-15 Impact factor: 38.330
Authors: Victor Guryev; Peter M Lansdorp; Vincent C T Hanlon; Carl-Adam Mattsson; Diana C J Spierings Journal: BMC Genomics Date: 2021-07-31 Impact factor: 3.969