Table 1. Current computational methods for meta'omic analysis.
| Method | Description | Reference |
|---|---|---|
| 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 | De Brujin graph coverage and connectivity | (Namiki et al, 2012) |
| MOCAT | Assembly and gene prediction toolkit | (Kultima et al, 2012) |
| SOAPdenovo | Single-genome assembler commonly tuned for metagenomes | (Li et al, 2010) |
| MetaORFA | Gene-targeted assembly approach | (Ye and Tang, 2009) |
| Taxonomic profiling | ||
| Amphora, Amphora2 | Automated pipeline for Phylogenomic Analysis | (Wu and Scott, 2012) |
| CARMA3 | Taxonomic classification of metagenomic shotgun sequences | (Gerlach and Stoye, 2011) |
| ClaMS | Classifier for Metagenomic Sequences | (Pati et al, 2011) |
| DiScRIBinATE | Distance Score Ratio for Improved Binning and Taxonomic Estimation | (Ghosh et al, 2010) |
| INDUS | Composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences | (Mohammed et al, 2011a) |
| MARTA | Suite of Java-based tools for assigning taxonomic status to DNA sequences | (Horton et al, 2010) |
| MetaCluster | Binning algorithm for high-throughput sequencing reads | (Wang et al, 2012) |
| MetaPhlAn | Profiles the composition of microbial communities from metagenomic shotgun sequencing data | (Segata et al, 2012) |
| MetaPhyler | Taxonomic classifier for metagenomic shotgun reads using phylogenetic marker reference genes | (Liu et al, 2011) |
| MTR | Taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks | (Gori et al, 2011) |
| NBC | Naive Bayes Classification tool for taxonomic assignment | (Rosen et al, 2011) |
| PaPaRa | Aligning short reads to reference alignments and trees | (Berger and Stamatakis, 2011) |
| PhyloPythia | Accurate phylogenetic classification of variable-length DNA fragments | (Patil et al, 2012) |
| Phymm, PhymmBL | Classification system designed for metagenomics experiments that assigns taxonomic labels to short DNA reads | (Brady and Salzberg, 2011) |
| RAIphy | Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles | (Nalbantoglu et al, 2011) |
| RITA | Classifying short genomic fragments from novel lineages using composition and homology | (Parks et al, 2011) |
| SOrt-ITEMS | Sequence orthology-based approach for improved taxonomic estimation of metagenomic sequences | (Monzoorul Haque et al, 2009) |
| SPHINX | Algorithm for taxonomic binning of metagenomic sequences | (Mohammed et al, 2011b) |
| TACOA | Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach | (Diaz et al, 2009) |
| Treephyler | Fast taxonomic profiling of metagenomes | (Schreiber et al, 2010) |
| Functional profiling | ||
| HUMAnN | Determines the presence/absence and abundance of microbial pathways in meta'omic data | (Abubucker et al, 2012) |
| metaSHARK | A web platform for interactive exploration of metabolic networks | (Hyland et al, 2006) |
| PRMT | Predicted Relative Metabolomic Turnover: determining metabolic turnover from a coastal marine metagenomic dataset | (Larsen et al, 2011) |
| RAMMCAP | Rapid analysis of Multiple Metagenomes with Clustering and Annotation Pipeline | (Li, 2009) |
| Interaction networks | ||
| SparCC | Estimates correlation values from compositional data for network inference | (Friedman and Alm, 2012) |
| CCREPE | Predicts microbial relationships within and between microbial habitats for network inference | (Faust et al, 2012) |
| Single-cell sequencing | ||
| IDBA-UD | Assembler for single-cell or metagenomic sequencing with uneven depths | (Peng et al, 2012) |
| SmashCell | Software framework for the analysis of single-cell amplified genome sequences | (Harrington et al, 2010) |
| Simulators | ||
| GemSIM | Error-model based simulator of next-generation sequencing data | (McElroy et al, 2012) |
| MetaSim | A sequencing simulator for genomics and metagenomics | (Richter et al, 2008) |
| Statistical tests | ||
| Metastats | Statistical analysis software for comparing metagenomic samples | (White et al, 2009) |
| LefSe | Nonparametric test for biomarker discovery in proportional microbial community data | (Segata et al, 2011) |
| ShotgunFunctionalizeR | A statistical test based on a Poisson model for metagenomic functional comparisons | (Kristiansson et al, 2009) |
| SourceTracker | A Bayesian approach to identify and quantify contaminants in a given community | (Knights et al, 2011) |
| General toolkit | ||
| CAMERA | Dashboard for environmental metagenomic and genomic data, metadata, and comparative analysis tools | (Seshadri et al, 2007) |
| IMG/M | Integrated metagenome data management and comparative analysis system | (Markowitz et al, 2012b) |
| MEGAN | Software for metagenomic, metatranscriptomic, metaproteomic, and rRNA analysis | (Huson et al, 2007) |
| METAREP | Online storage and analysis environment for meta'omic data | (Goll et al, 2010) |
| MG-RAST | Storage, quality control, annotation and comparison of meta'omic samples. | (Meyer et al, 2008) |
| SmashCommunity | Stand-alone annotation and analysis pipeline suitable for meta'omic data | (Arumugam et al, 2010) |
| STAMP | Comparative meta'omics software package | (Parks and Beiko, 2010) |
| VAMPS | Visualization and analysis of microbial population structure | (Huse et al, 2008) |
Common steps needed for metagenome and metatranscriptome interpretation include assembly, taxonomic profiling, functional profiling, ecological interaction network construction, single-cell sequencing, synthetic data simulators, and downstream statistical tests.