An ORFome assembly approach to metagenomics sequences analysis.

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Computational meta'omics for microbial community studies (2013, methodology): “Assembly Genovo Generative probabilistic model of reads (Laserson et al, 2011) khmer Probabilistic de Bruijn graphs (Pell et al, 2012) Meta-IDBA De Bruijn graph multiple alignments (Peng et al, 2011) metAMOS A Modular Open-Source Assembler component for metagenomes (Treangen et al, 2011a) MetaVelvet”
A Primer on Metagenomics (2010, methodology): “Nevertheless, for many practical purposes this method is very useful, because it appears to have a better recovery rate, for coding regions only, than regular, whole genome assemblers [56].”
The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics (2015, methodology): “This has been implemented by Ye and Tang (2008) in the MetaORFA pipeline, where the translations (ORFome) are used to search homologs in the databases ( Table 2 ).”
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads (2011, unknown): “…there are two tentative approaches to “de novo” analysis for the mixture of sequence reads from the environmental genomes: (i) applying a single-genome as-sembler to metagenome sequence reads [18, 4, 2, 26], and (ii) binning (clustering) a set of sequence reads into diﬀer-ent clusters [20, 25].”