Yu-Wei Wu1, Blake A Simmons2, Steven W Singer1. 1. Joint BioEnergy Institute, Emeryville, CA 94608, USA, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA and. 2. Joint BioEnergy Institute, Emeryville, CA 94608, USA, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA and Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA 94551, USA.
Abstract
UNLABELLED: The recovery of genomes from metagenomic datasets is a critical step to defining the functional roles of the underlying uncultivated populations. We previously developed MaxBin, an automated binning approach for high-throughput recovery of microbial genomes from metagenomes. Here we present an expanded binning algorithm, MaxBin 2.0, which recovers genomes from co-assembly of a collection of metagenomic datasets. Tests on simulated datasets revealed that MaxBin 2.0 is highly accurate in recovering individual genomes, and the application of MaxBin 2.0 to several metagenomes from environmental samples demonstrated that it could achieve two complementary goals: recovering more bacterial genomes compared to binning a single sample as well as comparing the microbial community composition between different sampling environments. AVAILABILITY AND IMPLEMENTATION: MaxBin 2.0 is freely available at http://sourceforge.net/projects/maxbin/ under BSD license.
UNLABELLED: The recovery of genomes from metagenomic datasets is a critical step to defining the functional roles of the underlying uncultivated populations. We previously developed MaxBin, an automated binning approach for high-throughput recovery of microbial genomes from metagenomes. Here we present an expanded binning algorithm, MaxBin 2.0, which recovers genomes from co-assembly of a collection of metagenomic datasets. Tests on simulated datasets revealed that MaxBin 2.0 is highly accurate in recovering individual genomes, and the application of MaxBin 2.0 to several metagenomes from environmental samples demonstrated that it could achieve two complementary goals: recovering more bacterial genomes compared to binning a single sample as well as comparing the microbial community composition between different sampling environments. AVAILABILITY AND IMPLEMENTATION: MaxBin 2.0 is freely available at http://sourceforge.net/projects/maxbin/ under BSD license.
Authors: Laura C Valk; Jeroen Frank; Pilar de la Torre-Cortés; Max van 't Hof; Antonius J A van Maris; Jack T Pronk; Mark C M van Loosdrecht Journal: Appl Environ Microbiol Date: 2018-08-31 Impact factor: 4.792
Authors: Michiel H In 't Zandt; Nardy Kip; Jeroen Frank; Stefan Jansen; Johannes A van Veen; Mike S M Jetten; Cornelia U Welte Journal: Appl Environ Microbiol Date: 2019-10-01 Impact factor: 4.792
Authors: Katharina Kitzinger; Cory C Padilla; Hannah K Marchant; Philipp F Hach; Craig W Herbold; Abiel T Kidane; Martin Könneke; Sten Littmann; Maria Mooshammer; Jutta Niggemann; Sandra Petrov; Andreas Richter; Frank J Stewart; Michael Wagner; Marcel M M Kuypers; Laura A Bristow Journal: Nat Microbiol Date: 2018-12-10 Impact factor: 17.745
Authors: Eric R Johnston; Janet K Hatt; Zhili He; Liyou Wu; Xue Guo; Yiqi Luo; Edward A G Schuur; James M Tiedje; Jizhong Zhou; Konstantinos T Konstantinidis Journal: Proc Natl Acad Sci U S A Date: 2019-07-08 Impact factor: 11.205
Authors: Jakob Nybo Nissen; Joachim Johansen; Rosa Lundbye Allesøe; Casper Kaae Sønderby; Jose Juan Almagro Armenteros; Christopher Heje Grønbech; Lars Juhl Jensen; Henrik Bjørn Nielsen; Thomas Nordahl Petersen; Ole Winther; Simon Rasmussen Journal: Nat Biotechnol Date: 2021-01-04 Impact factor: 54.908
Authors: Sean K Bay; Xiyang Dong; James A Bradley; Pok Man Leung; Rhys Grinter; Thanavit Jirapanjawat; Stefan K Arndt; Perran L M Cook; Douglas E LaRowe; Philipp A Nauer; Eleonora Chiri; Chris Greening Journal: Nat Microbiol Date: 2021-01-04 Impact factor: 17.745
Authors: Ping Hu; Eric A Dubinsky; Alexander J Probst; Jian Wang; Christian M K Sieber; Lauren M Tom; Piero R Gardinali; Jillian F Banfield; Ronald M Atlas; Gary L Andersen Journal: Proc Natl Acad Sci U S A Date: 2017-06-26 Impact factor: 11.205