Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

(2013) Todd J Treangen et al.   GENOME BIOLOGY

Reference-independent comparative metagenomics using cross-assembly: crAss

(2012) Bas E. Dutilh et al.   BIOINFORMATICS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

In Situ Evolutionary Rate Measurements Show Ecological Success of Recently Emerged Bacterial Hybrids

(2012) V. J. Denef et al.   SCIENCE

Metagenomic Analysis of Kimchi, a Traditional Korean Fermented Food

(2011) Ji Young Jung et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Meta-IDBA: a de Novo assembler for metagenomic data

(2011) Y. Peng et al.   BIOINFORMATICS

Bambus 2: scaffolding metagenomes

(2011) Sergey Koren et al.   BIOINFORMATICS

Classifying short genomic fragments from novel lineages using composition and homology

(2011) Donovan H Parks et al.   BMC BIOINFORMATICS

Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph

(2011) Z. Li et al.   Briefings in Functional Genomics

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs

(2010) Vamsi K Kundeti et al.   BMC BIOINFORMATICS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

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

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

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

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

Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems

(2008) A. L. Davidson et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE