QIIME allows analysis of high-throughput community sequencing data

Nature Methods, Год журнала: 2010, Номер 7(5), С. 335 - 336

Опубликована: Апрель 11, 2010

Язык: Английский

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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Nucleic Acids Research, Год журнала: 2012, Номер 41(D1), С. D590 - D596

Опубликована: Ноя. 27, 2012

SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit 288 717 large rRNA sequences. Since initial description project, substantial new features have been introduced, including advanced quality control procedures, an improved aligner, tools probe primer evaluation optimized browsing, searching downloading on website. Furthermore, extensively curated taxonomy non-redundant datasets provide ideal reference high-throughput classification data next-generation sequencing approaches.

Язык: Английский

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DADA2: High-resolution sample inference from Illumina amplicon data

Nature Methods, Год журнала: 2016, Номер 13(7), С. 581 - 583

Опубликована: Май 23, 2016

Язык: Английский

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

PLoS ONE, Год журнала: 2013, Номер 8(4), С. e61217 - e61217

Опубликована: Апрель 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.

Язык: Английский

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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Nature Biotechnology, Год журнала: 2019, Номер 37(8), С. 852 - 857

Опубликована: Июль 24, 2019

Язык: Английский

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Metagenomic biomarker discovery and explanation

Genome biology, Год журнала: 2011, Номер 12(6)

Опубликована: Июнь 24, 2011

Abstract This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests biological consistency effect size estimation. addresses the challenge finding organisms, genes, or pathways that consistently explain differences between two more microbial communities, which is central problem to metagenomics. We extensively validate our on several microbiomes convenient online interface provided at http://huttenhower.sph.harvard.edu/lefse/ .

Язык: Английский

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VSEARCH: a versatile open source tool for metagenomics

PeerJ, Год журнала: 2016, Номер 4, С. e2584 - e2584

Опубликована: Окт. 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.

Язык: 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, Год журнала: 2013, Номер 79(17), С. 5112 - 5120

Опубликована: Июнь 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.

Язык: Английский

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Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

Proceedings of the National Academy of Sciences, Год журнала: 2010, Номер 107(33), С. 14691 - 14696

Опубликована: Авг. 2, 2010

Gut microbial composition depends on different dietary habits just as health metabolism, but the association of microbiota with diets in human populations has not yet been shown. In this work, we compared fecal European children (EU) and that from a rural African village Burkina Faso (BF), where diet, high fiber content, is similar to early settlements at time birth agriculture. By using high-throughput 16S rDNA sequencing biochemical analyses, found significant differences gut between two groups. BF showed enrichment Bacteroidetes depletion Firmicutes ( P < 0.001), unique abundance bacteria genus Prevotella Xylanibacter , known contain set bacterial genes for cellulose xylan hydrolysis, completely lacking EU children. addition, significantly more short-chain fatty acids 0.001) than Also, Enterobacteriaceae Shigella Escherichia) were underrepresented 0.05). We hypothesize coevolved polysaccharide-rich diet individuals, allowing them maximize energy intake fibers while also protecting inflammations noninfectious colonic diseases. This study investigates compares intestinal characterized by modern western indicating importance preserving treasure diversity ancient communities worldwide.

Язык: Английский

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Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Proceedings of the National Academy of Sciences, Год журнала: 2012, Номер 109(16), С. 6241 - 6246

Опубликована: Март 27, 2012

Six DNA regions were evaluated as potential barcodes for Fungi , the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region mitochondrial cytochrome c oxidase subunit 1 used animal barcode was excluded marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from nuclear ribosomal RNA cistron compared together with three representative protein-coding genes (largest polymerase II, minichromosome maintenance protein). Although gene had higher percent correct identification markers, low PCR amplification sequencing success eliminated them candidates universal fungal barcode. Among cistron, internal transcribed spacer (ITS) has highest probability successful broadest range most clearly defined gap between inter- intraspecific variation. subunit, popular phylogenetic marker certain groups, superior species resolution some taxonomic such early diverging lineages ascomycete yeasts, but otherwise slightly inferior ITS. small poor species-level fungi. ITS will formally proposed adoption primary Consortium Barcode Life, possibility that supplementary may developed particular narrowly circumscribed groups.

Язык: Английский

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