Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis

Scholz, Matthew; Lo, Chien-Chi; Chain, Patrick

doi:10.1016/j.copbio.2011.11.013

Cited by 312 publications

(225 citation statements)

References 53 publications

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“…Metagenomes from rumen, human gut, and permafrost soil sequencing could be assembled only by discarding low-abundance sequences before assembly (2,4,5). Although many metagenome-specific assemblers have been developed recently for the assembly of low-complexity communities, they cannot work with the volume of reads necessary to achieve high coverage for extremely diverse environmental metagenomes (10)(11)(12).…”

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confidence: 99%

Tackling soil diversity with the assembly of large, complex metagenomes

Howe

Jansson

Malfatti

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

301

275

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Significance Investigations of complex environments rely on large volumes of sequence data to adequately sample the genetic diversity of a microbial community. The assembly of short-read data into longer, more interpretable sequence currently is not possible for much of the research community because it requires specialized computational facilities. We present approaches that make de novo assembly of complex metagenomes more accessible. These approaches scale data size with community richness and subdivide the data into tractable subsets representing individual species. We applied these methods toward the assembly of two large soil metagenomes to identify important metagenomic references and show that considerably more data are needed to study the terrestrial microbiome comprehensively.

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mentioning

confidence: 99%

Tackling soil diversity with the assembly of large, complex metagenomes

Howe

Jansson

Malfatti

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

301

275

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“…The HTS approach is greatly influenced, indeed driven, by analysis of sequences (39). Several open-source programs are available for processing 16S amplicon HTS data (40)(41)(42).…”

Section: Critical Issuesmentioning

confidence: 99%

High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

Ercolini

2013

Appl Environ Microbiol

414

229

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Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described.

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“…Postsequencing processing is applied to raw sequence data to perform quality control (QC), filter reads for contamination, map reads toward relevant genomes, assemble genomes (or partial genomes), and perform homology searches and taxonomic/phylogenetic studies. 29,64,65 This is shown in Figure 2 as a flowchart of methodologies and implementation of methodologies for analysis. Quality of datasets for metagenomic analysis consists of several parts.…”

Section: Bioinformatics and Processing Of Datamentioning

confidence: 99%