BACKGROUND: Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem. RESULTS: Existing algorithms are largely optimized for speed and coverage; in contrast, we present here a software framework that focuses on a restricted set of informative gene families, using Maximum Likelihood to assign these with the best possible accuracy. This framework ('MLTreeMap'; http://mltreemap.org/) uses raw nucleotide sequences as input, and includes hand-curated, extensible reference information. CONCLUSIONS: We discuss how we validated our pipeline using complete genomes as well as simulated and actual environmental sequences.
BACKGROUND: Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem. RESULTS: Existing algorithms are largely optimized for speed and coverage; in contrast, we present here a software framework that focuses on a restricted set of informative gene families, using Maximum Likelihood to assign these with the best possible accuracy. This framework ('MLTreeMap'; http://mltreemap.org/) uses raw nucleotide sequences as input, and includes hand-curated, extensible reference information. CONCLUSIONS: We discuss how we validated our pipeline using complete genomes as well as simulated and actual environmental sequences.
Authors: Claudia Knief; Nathanaël Delmotte; Samuel Chaffron; Manuel Stark; Gerd Innerebner; Reiner Wassmann; Christian von Mering; Julia A Vorholt Journal: ISME J Date: 2011-12-22 Impact factor: 10.302
Authors: Kaston Leung; Hans Zahn; Timothy Leaver; Kishori M Konwar; Niels W Hanson; Antoine P Pagé; Chien-Chi Lo; Patrick S Chain; Steven J Hallam; Carl L Hansen Journal: Proc Natl Acad Sci U S A Date: 2012-04-30 Impact factor: 11.205
Authors: Daniel H Huson; Suparna Mitra; Hans-Joachim Ruscheweyh; Nico Weber; Stephan C Schuster Journal: Genome Res Date: 2011-06-20 Impact factor: 9.043
Authors: Robert Lücking; M Catherine Aime; Barbara Robbertse; Andrew N Miller; Hiran A Ariyawansa; Takayuki Aoki; Gianluigi Cardinali; Pedro W Crous; Irina S Druzhinina; David M Geiser; David L Hawksworth; Kevin D Hyde; Laszlo Irinyi; Rajesh Jeewon; Peter R Johnston; Paul M Kirk; Elaine Malosso; Tom W May; Wieland Meyer; Maarja Öpik; Vincent Robert; Marc Stadler; Marco Thines; Duong Vu; Andrey M Yurkov; Ning Zhang; Conrad L Schoch Journal: IMA Fungus Date: 2020-07-10 Impact factor: 3.515
Authors: Bilal Wajid; Faria Anwar; Imran Wajid; Haseeb Nisar; Sharoze Meraj; Ali Zafar; Mustafa Kamal Al-Shawaqfeh; Ali Riza Ekti; Asia Khatoon; Jan S Suchodolski Journal: Funct Integr Genomics Date: 2021-10-18 Impact factor: 3.410