QIIME allows analysis of high-throughput community sequencing data
Nature MethodsPublished 11 April 2010
J. Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D. Bushman, Elizabeth K. Costello
Citations35,169
SJR quartileQ1
SJR score17.25
SNIP8.40
Generate an AI Snapshot to get a quick, structured summary of this paper.
Study Snapshot
ObjectiveStudy objective
MethodsResearch methodology
PopulationPopulation studied
Sample sizeSample sizes
OutcomesStudy outcomes here
ResultsStudy results comes here
LimitationsResearch study limitations comes here
A concise AI-generated summary of the paper will appear here once you click Generate AI Snapshot.
TL;DR
An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
Keywords
Biochemistry, Genetics and Molecular BiologyEnvironmental Science
Applied and Environmental MicrobiologyIntroducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
21,757 Citations2009Patrick D. Schloss, Sarah L. Westcott +13 more
M mothur is used as a case study to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments.
Nucleic Acids ResearchThe Ribosomal Database Project: improved alignments and new tools for rRNA analysis
4,821 Citations2008James R. Cole, Qi Wang +9 more
An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences, and a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data.
Genome ResearchThe NIH Human Microbiome Project
2,070 Citations2009The NIH HMP Working Group, Jane L. Peterson +38 more
The ultimate objective of the HMP is to demonstrate that there are opportunities to improve human health through monitoring or manipulation of the human microbiome.
Nature MethodsError-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
1,322 Citations2008Micah Hamady, Jeffrey J. Walker +3 more
Using error-correcting DNA barcodes, one run of a massively parallel pyrosequencer is constructed that characterized nearly as many 16S rRNA genes as have been sequenced to date by Sanger sequencing.
Genome biologyPyCogent: a toolkit for making sense from sequence
208 Citations2007Rob Knight, Peter Maxwell +19 more
The COmparative GENomic Toolkit is implemented in Python, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics.