SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control

Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research

(2017) André M. Comeau et al.   mSystems

Captivity humanizes the primate microbiome

(2016) Jonathan B. Clayton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes

(2016) Gabriel A. Al-Ghalith et al.   PLoS Computational Biology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Experimental and analytical tools for studying the human microbiome

(2011) Justin Kuczynski et al.   NATURE REVIEWS GENETICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

What would you do if you could sequence everything?

(2008) Avak Kahvejian et al.   NATURE BIOTECHNOLOGY

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

(2008) Micah Hamady et al.   NATURE METHODS

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH