DADA2: High-resolution sample inference from Illumina amplicon data

Nature Methods, Journal Year: 2016, Volume and Issue: 13(7), P. 581 - 583

Published: May 23, 2016

Language: Английский

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phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

PLoS ONE, Journal Year: 2013, Volume and Issue: 8(4), P. e61217 - e61217

Published: April 22, 2013

Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration different types data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With increased breadth experimental designs now being pursued, project-specific statistical analyses are often needed, these difficult (or impossible) for peer researchers to independently reproduce. vast majority requisite tools performing reproducibly already implemented in R its extensions (packages), but limited support high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated object-oriented representation R. It supports importing variety common formats, as well techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, production publication-quality graphics; all manner that is easy document, share, modify. We show how apply functions other packages phyloseq-represented data, illustrating availability large number open source discuss use phyloseq reproducible research, practice fields still rare highly parallel have made available materials necessary completely reproduce figures included this article, an example best practices research. Conclusions project new open-source package, freely on web both GitHub Bioconductor.

Language: Английский

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UPARSE: highly accurate OTU sequences from microbial amplicon reads

Nature Methods, Journal Year: 2013, Volume and Issue: 10(10), P. 996 - 998

Published: Aug. 18, 2013

Language: Английский

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VSEARCH: a versatile open source tool for metagenomics

PeerJ, Journal Year: 2016, Volume and Issue: 4, P. e2584 - e2584

Published: Oct. 18, 2016

VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing preparing metagenomics, genomics population nucleotide sequence data. It designed as alternative to the widely used USEARCH (Edgar, 2010) which code not publicly available, algorithm details are only rudimentarily described, a memory-confined 32-bit version freely available academic use.When searching sequences, uses fast heuristic based on words shared by query target sequences in order quickly identify similar strategy probably USEARCH. then performs optimal global alignment against potential using full dynamic programming instead seed-and-extend Pairwise alignments computed parallel vectorisation multiple threads.VSEARCH includes most commands analysing 7 several those 8, including (exact or alignment), clustering similarity (using length pre-sorting, abundance pre-sorting user-defined order), chimera detection (reference-based de novo), dereplication (full prefix), pairwise alignment, reverse complementation, sorting, subsampling. also FASTQ file processing, i.e., format detection, filtering, read quality statistics, merging paired reads. Furthermore, extends functionality with new improvements, shuffling, rereplication, masking low-complexity well-known DUST algorithm, choice among different definitions, conversion. here shown be more accurate than when performing searching, clustering, subsampling, while par paired-ends merging. slower but significantly faster paired-end reads dereplication. at https://github.com/torognes/vsearch under either BSD 2-clause license GNU General Public License 3.0.VSEARCH has been fast, full-fledged A open-source versatile analysis now metagenomics community.

Language: Английский

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Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

Nature Biotechnology, Journal Year: 2013, Volume and Issue: 31(9), P. 814 - 821

Published: Aug. 25, 2013

Language: Английский

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Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

Applied and Environmental Microbiology, Journal Year: 2013, Volume and Issue: 79(17), P. 5112 - 5120

Published: June 22, 2013

Rapid advances in sequencing technology have changed the experimental landscape of microbial ecology. In last 10 years, field has moved from hundreds 16S rRNA gene fragments per study using clone libraries to millions next-generation technologies 454 and Illumina. As these advance, it is critical assess strengths, weaknesses, overall suitability platforms for interrogation communities. Here, we present an improved method variable regions within Illumina's MiSeq platform, which currently capable producing paired 250-nucleotide reads. We evaluated three overlapping that vary length (i.e., V34, V4, V45) by resequencing a mock community natural samples human feces, mouse soil. By titrating concentration amplicons applied flow cell quality score-based approach correct discrepancies between reads used construct contigs, were able reduce error rates as much two orders magnitude. Finally, reprocessed previous demonstrate large numbers could be multiplexed sequenced parallel with shotgun metagenomes. These analyses our can provide data are at least good generated platform while providing considerably higher coverage fraction cost.

Language: Английский

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A metagenome-wide association study of gut microbiota in type 2 diabetes

Nature, Journal Year: 2012, Volume and Issue: 490(7418), P. 55 - 60

Published: Sept. 25, 2012

Language: Английский

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Diversity, stability and resilience of the human gut microbiota

Nature, Journal Year: 2012, Volume and Issue: 489(7415), P. 220 - 230

Published: Sept. 1, 2012

Language: Английский

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The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic T _reg Cell Homeostasis

Science, Journal Year: 2013, Volume and Issue: 341(6145), P. 569 - 573

Published: July 5, 2013

Regulatory T cells (Tregs) that express the transcription factor Foxp3 are critical for regulating intestinal inflammation. Candidate microbe approaches have identified bacterial species and strain-specific molecules can affect immune responses, including modulate Treg responses. Because neither all humans nor mice harbor same strains, we posited more prevalent factors exist regulate number function of colonic Tregs. We determined short-chain fatty acids, gut microbiota-derived fermentation products, size pool protect against colitis in a Ffar2-dependent manner mice. Our study reveals class abundant microbial metabolites underlies adaptive microbiota coadaptation promotes homeostasis health.

Language: Английский

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Kraken: ultrafast metagenomic sequence classification using exact alignments

Genome biology, Journal Year: 2014, Volume and Issue: 15(3)

Published: March 3, 2014

Abstract Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed this task have been relatively slow computationally expensive, forcing researchers use faster abundance estimation programs, which only classify small subsets of data. Using exact alignment k -mers, achieves classification accuracy comparable the fastest BLAST program. In its mode, classifies 100 base pair reads at a rate over 4.1 million per minute, 909 times than Megablast 11 MetaPhlAn. available http://ccb.jhu.edu/software/kraken/ .

Language: Английский

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