Mikko Rautiainen1,2,3, Tobias Marschall4. 1. Center for Bioinformatics, Saarland University, Saarbrücken, Germany. 2. Max Planck Institute for Informatics, Saarbrücken, Germany. 3. Saarbrücken Graduate School for Computer Science, Saarbrücken, Germany. 4. Heinrich Heine University Düsseldorf, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Germany Düsseldorf.
Abstract
MOTIVATION: De Bruijn graphs can be constructed from short reads efficiently and have been used for many purposes. Traditionally long read sequencing technologies have had too high error rates for de Bruijn graph-based methods. Recently, HiFi reads have provided a combination of long read length and low error rate, which enables de Bruijn graphs to be used with HiFi reads. RESULTS: We have implemented MBG, a tool for building sparse de Bruijn graphs from HiFi reads. MBG outperforms existing tools for building dense de Bruijn graphs, and can build a graph of 50x coverage whole human genome HiFi reads in four hours on a single core. MBG also assembles the bacterial E. coli genome into a single contig in 8 seconds. AVAILABILITY: Package manager: https://anaconda.org/bioconda/mbg and source code: https://github.com/maickrau/MBG. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: De Bruijn graphs can be constructed from short reads efficiently and have been used for many purposes. Traditionally long read sequencing technologies have had too high error rates for de Bruijn graph-based methods. Recently, HiFi reads have provided a combination of long read length and low error rate, which enables de Bruijn graphs to be used with HiFi reads. RESULTS: We have implemented MBG, a tool for building sparse de Bruijn graphs from HiFi reads. MBG outperforms existing tools for building dense de Bruijn graphs, and can build a graph of 50x coverage whole human genome HiFi reads in four hours on a single core. MBG also assembles the bacterial E. coli genome into a single contig in 8 seconds. AVAILABILITY: Package manager: https://anaconda.org/bioconda/mbg and source code: https://github.com/maickrau/MBG. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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