Dataset Information

A-GAME: improving the assembly of pooled functional metagenomics sequence data.

ABSTRACT:

Background

Expression screening of environmental DNA (eDNA) libraries is a popular approach for the identification and characterization of novel microbial enzymes with promising biotechnological properties. In such "functional metagenomics" experiments, inserts, selected on the basis of activity assays, are sequenced with high throughput sequencing technologies. Assembly is followed by gene prediction, annotation and identification of candidate genes that are subsequently evaluated for biotechnological applications.

Results

Here we present A-GAME (A GAlaxy suite for functional MEtagenomics), a web service incorporating state of the art tools and workflows for the analysis of eDNA sequence data. We illustrate the potential of A-GAME workflows using real functional metagenomics data, showing that they outperform alternative metagenomics assemblers. Dedicated tools available in A-GAME allow efficient analysis of pooled libraries and rapid identification of candidate genes, reducing sequencing costs and saving the need for laborious manual annotation.

Conclusion

In conclusion, we believe A-GAME will constitute a valuable resource for the functional metagenomics community. A-GAME is publicly available at http://beaconlab.it/agame.

SUBMITTER: Chiara M

PROVIDER: S-EPMC5767027 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A-GAME: improving the assembly of pooled functional metagenomics sequence data.

Chiara Matteo M Placido Antonio A Picardi Ernesto E Ceci Luigi Ruggiero LR Horner David Stephen DS Pesole Graziano G

BMC genomics 20180112 1

<h4>Background</h4>Expression screening of environmental DNA (eDNA) libraries is a popular approach for the identification and characterization of novel microbial enzymes with promising biotechnological properties. In such "functional metagenomics" experiments, inserts, selected on the basis of activity assays, are sequenced with high throughput sequencing technologies. Assembly is followed by gene prediction, annotation and identification of candidate genes that are subsequently evaluated for b ...[more]

PMID: 29329522

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Dataset Information

A-GAME: improving the assembly of pooled functional metagenomics sequence data.

Background

Results

Conclusion

Publications

A-GAME: improving the assembly of pooled functional metagenomics sequence data.

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