Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

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

(2011) Ozkan U Nalbantoglu et al.   BMC BIOINFORMATICS

Genovo: De Novo Assembly for Metagenomes

(2011) Jonathan Laserson et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

DiScRIBinATE: a rapid method for accurate taxonomic classification of metagenomic sequences

(2010) Tarini Ghosh 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

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

Metagenomics: Facts and Artifacts, and Computational Challenges

(2010) John C. Wooley et al.   JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins

(2010) P. J. Turnbaugh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Naryttza N Diaz et al.   BMC BIOINFORMATICS

Genome assembly reborn: recent computational challenges

(2009) M. Pop   BRIEFINGS IN BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

(2009) Konstantinos Liolios et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

High Diversity of the Viral Community from an Antarctic Lake

(2009) A. Lopez-Bueno et al.   SCIENCE

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

(2009) Jan O Korbel et al.   GENOME BIOLOGY

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

(2009) Iain MacCallum et al.   GENOME BIOLOGY

AN ORFOME ASSEMBLY APPROACH TO METAGENOMICS SEQUENCES ANALYSIS

(2009) YUZHEN YE et al.   Journal of Bioinformatics and Computational Biology

Assembly of Viral Metagenomes from Yellowstone Hot Springs

(2008) T. Schoenfeld et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomics: Read Length Matters

(2008) K. E. Wommack et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer

(2008) D. Hernandez et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Phylogenetic classification of short environmental DNA fragments

(2008) Lutz Krause et al.   NUCLEIC ACIDS RESEARCH

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm 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

Short read fragment assembly of bacterial genomes

(2007) M. J. Chaisson et al.   GENOME RESEARCH