SmashCommunity: a metagenomic annotation and analysis tool

Arumugam, Manimozhiyan; Harrington, Eoghan; Foerstner, Konrad; Raes, Jeroen; Bork, Peer

doi:10.1093/bioinformatics/btq536

Cited by 91 publications

(55 citation statements)

References 17 publications

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“…Some software packages exist to tie together various components, and although no single standard exists yet, the Genomic Standards Consortium 92 is currently working towards a consistent way for describing and comparing approaches. Depending on the need for customization and computational resources, annotation pipelines can be downloaded and run on a local computer cluster (for example, SmashCommunity 93 ), or a user can upload their sequence data to a Web server and use a pre-structured pipeline, such as MG-RAST 71 , CAMERA 94 or IMG/M 95 . One major benefit of online resources such as MG-RAST is the ability to compare publicly available metagenomic data sets, allowing users to perform comparative metagenomic analysis of their samples against a huge variety of environmental and host-associated metagenomic projects.…”

Section: Bioinformatics Data Analysis Toolsmentioning

confidence: 99%

Experimental and analytical tools for studying the human microbiome

et al. 2011

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The human microbiome substantially affects many aspects of human physiology, including metabolism, drug interactions and numerous diseases. This realization, coupled with ever-improving nucleotide sequencing technology, has precipitated the collection of diverse data sets that profile the microbiome. In the past 2 years, studies have begun to include sufficient numbers of subjects to provide the power to associate these microbiome features with clinical states using advanced algorithms, increasing the use of microbiome studies both individually and collectively. Here we discuss tools and strategies for microbiome studies, from primer selection to bioinformatics analysis.

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Section: Bioinformatics Data Analysis Toolsmentioning

confidence: 99%

Experimental and analytical tools for studying the human microbiome

et al. 2011

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“…Some examples are IMG/M, CAMERA, MG-RAST, METArep, SmashCommunity, GAAS and MEGAN (Markowitz et al, 2008;Meyer et al, 2008;Angly et al, 2009;Huson et al, 2009;Arumugam et al, 2010;Goll et al, 2010;Sun et al, 2011) (Table 1).…”

Section: Metabolic Reconstructionmentioning

confidence: 99%

Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches

Logares

Haverkamp

Kumar

et al. 2012

Journal of Microbiological Methods

119

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“…These include stand-alone software such as MEGAN [6], HUMAnN [7], RAMMCAP [8], SmashCommunity [9], and MOCAT [10], as well as cloud-based tools like CloVR [11], and web portals like MG-RAST [12], MicrobesOnline [13], and the IMG/M annotation server [14](S1 Table). Generally, these methods operate by comparing metagenomic sequence reads to a reference database of functionally annotated protein families and use homology inference to annotate each read [5].…”

Section: Introductionmentioning

confidence: 99%

Automated and accurate estimation of gene family abundance from shotgun metagenomes

Nayfach

Bradley

Wyman

et al. 2015

Preprint

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Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw inferences about the functional potential of the community and to identify putative functional biomarkers. However, little is known about how decisions made during annotation affect the reliability of the results. Here, we use statistical simulations to rigorously assess how to optimize annotation accuracy and speed, given parameters of the input data like read length and library size. We identify best practices in metagenome annotation and use them to guide the development of the Shotgun Metagenome Annotation Pipeline (ShotMAP). ShotMAP is an analytically flexible, end-to-end annotation pipeline that can be implemented either on a local computer or a cloud compute cluster. We use ShotMAP to assess how different annotation databases impact the interpretation of how marine metagenome and metatranscriptome functional capacity changes across seasons. We also apply ShotMAP to data obtained from a clinical microbiome investigation of inflammatory bowel disease. This analysis finds that gut microbiota collected from Crohn's disease patients are functionally distinct from gut microbiota collected from either ulcerative colitis patients or healthy controls, with differential abundance of metabolic pathways related to host-microbiome interactions that may serve as putative biomarkers of disease. Author SummaryMicrobial communities perform a wide variety of functions, from marine photosynthesis to aiding digestion in the human gut. Shotgun "metagenomic" sequencing can be used to sample millions of short DNA sequences from such communities directly, without needing to first culture its constituents in the laboratory. Using these data, researchers can survey which functions are encoded by mapping these short sequences to known protein families and pathways. Several tools for this annotation already exist. But, annotation is a multi-step process that includes identification of genes in a metagenome and determination of the type of protein each gene encodes. We currently know little about how different choices of parameters during annotation influences the final results. In this work, we systematically test how several key decisions affect the accuracy and speed of annotation, and based on these results, develop new software for annotation, which we named ShotMAP. We then use ShotMAP to functionally characterize marine communities and gut communities in a clinical cohort of inflammatory bowel disease. We find several functions are differentially represented in the gut microbiome of Crohn's disease patients, which could be candidates for biomarkers and could also offer insight into the pathophysiology of Crohn's. ShotMAP is freely available (https://github.com/sharpton/shotmap).

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SmashCommunity: a metagenomic annotation and analysis tool

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 91 publications

References 17 publications

Experimental and analytical tools for studying the human microbiome

Experimental and analytical tools for studying the human microbiome

Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches

Automated and accurate estimation of gene family abundance from shotgun metagenomes

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