PhyloPythia and its successor PhyloPythiaS are fast and accurate oligomer signature-based classifiers for the taxonomic assignment of metagenome sequence fragments.
Metagenomics uses random shotgun sequencing to recover genome sequence information from microbial communities without the need for cultivation of its member species. It thus gives access to the vast portion of the microbial world that cannot be cultured with standard techniques (Hugenholtz 2002). The sequencing of randomly sheared microbial community DNA initially generates a collection of short sequence fragments called reads. Depending on the sequencing technology used, the amount of generated data and read lengths vary (Metzker 2010; Droge and McHardy 2012): while traditional Sanger sequencing generates reads of around 800 bp, the commercially available “next-generation” sequencing technologies return reads of approximately 50–75 bp (SOLID sequencing by Applied Biosciences/Life Technologies),...
- Droge J, McHardy AC. Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. Brief Bioinforma. 2012;13(6):646–55.Google Scholar
- Glass EM, Wilkening J, Wilke A, Antonopoulos D, Meyer F. Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harb Protoc. 2010; 2010(1):pdb prot5368.Google Scholar
- Hugenholtz P. Exploring prokaryotic diversity in the genomic era. Genome Biol. 2002;3(2):REVIEWS0003.Google Scholar
- Illumina. 2012. Available from: http://www.illumina.com/Documents/systems/hiseq/datasheet_hiseq_systems.pdf.
- Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Grechkin Y, et al. IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res. 2012;40(Database issue):D123–9.Google Scholar
- Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, et al. Community cyberinfrastructure for advanced microbial ecology research and analysis: the CAMERA resource. Nucleic Acids Res. 2011;39(Database issue):D546–51.Google Scholar
- Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, et al. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature. 2007;450(7169):560–5.Google Scholar