BMPOS: a Flexible and User-Friendly Tool Sets for Microbiome Studies

MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation

(2015) Yu-Chieh Liao et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Programming revisited

(2015) Thomas C. Schulthess   Nature Physics

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

(2015) Eric A. Franzosa et al.   NATURE REVIEWS MICROBIOLOGY

Data analysis for 16S microbial profiling from different benchtop sequencing platforms

(2014) Victor S. Pylro et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants

(2014) Brandon Brooks et al.   Microbiome

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Brazilian Microbiome Project: Revealing the Unexplored Microbial Diversity—Challenges and Prospects

(2013) Victor Satler Pylro et al.   MICROBIAL ECOLOGY

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

(2013) A. Murat Eren et al.   Methods in Ecology and Evolution

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

(2012) Daniel McDonald et al.   GigaScience

Pyrosequencing as a tool for better understanding of human microbiomes

(2012) José F. Siqueira et al.   Journal of Oral Microbiology

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Identifying biologically relevant differences between metagenomic communities

(2010) Donovan H. Parks et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY