Classification of metagenomic sequences: methods and challenges

A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio

(2011) H. C. M. Leung et al.   BIOINFORMATICS

Aligning short reads to reference alignments and trees

(2011) Simon A. Berger et al.   BIOINFORMATICS

RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles

(2011) Ozkan U Nalbantoglu et al.   BMC BIOINFORMATICS

Computational challenges of sequence classification in microbiomic data

(2011) P. Ribeca et al.   BRIEFINGS IN BIOINFORMATICS

The oral metagenome in health and disease

(2011) Pedro Belda-Ferre et al.   ISME Journal

Eu-Detect: An algorithm for detecting eukaryotic sequences in metagenomic data sets

(2011) Monzoorul Haque Mohammed et al.   JOURNAL OF BIOSCIENCES

A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-tuples

(2011) Yu-Wei Wu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

Metagenome of the gut of a malnourished child

(2011) Sourav Gupta et al.   Gut Pathogens

ClaMS: A Classifier for Metagenomic Sequences

(2011) Amrita Pati et al.   Standards in Genomic Sciences

Treephyler: fast taxonomic profiling of metagenomes

(2010) F. Schreiber et al.   BIOINFORMATICS

SPHINX—an algorithm for taxonomic binning of metagenomic sequences

(2010) Monzoorul Haque Mohammed et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

(2010) Manuel Stark et al.   BMC GENOMICS

Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium

(2010) Athanasios Lykidis et al.   ISME Journal

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

(2010) Jenna L. Morgan et al.   PLoS One

MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences

(2009) Matthew Horton et al.   BIOINFORMATICS

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences

(2009) M. Monzoorul Haque et al.   BIOINFORMATICS

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

(2009) Naryttza N Diaz et al.   BMC BIOINFORMATICS

On the origin of prokaryotic species

(2009) W. F. Doolittle et al.   GENOME RESEARCH

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Binning sequences using very sparse labels within a metagenome

(2008) Chon-Kit Chan et al.   BMC BIOINFORMATICS

Phylogenetic classification of short environmental DNA fragments

(2008) Lutz Krause et al.   NUCLEIC ACIDS RESEARCH

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

(2008) Daniel C. Richter et al.   PLoS One

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY