Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

Miguel Pignatelli; Andrés Moya

doi:10.1371/journal.pone.0019984

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Open Access

Peer-reviewed

Research Article

Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

Miguel Pignatelli ,

* E-mail: mp@ebi.ac.uk

Affiliations Unitat Mixta d'Investigació en Genòmica i Salut, Centre Superior d'Investigació en Salut Pública/UVEG-Institut Cavanilles, Valencia, Spain, CIBER en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
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Andrés Moya

Affiliations Unitat Mixta d'Investigació en Genòmica i Salut, Centre Superior d'Investigació en Salut Pública/UVEG-Institut Cavanilles, Valencia, Spain, CIBER en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
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Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

Miguel Pignatelli,
Andrés Moya

Published: May 23, 2011
https://doi.org/10.1371/journal.pone.0019984

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Functional assignment method

Posted by matram on 12 Feb 2012 at 09:51 GMT

I find this paper very useful and interesting, but I've got a curiosity that someone can maybe satisfy. The work is much confident on blast-based functional assignment. I was wondering what would have been the results with profile-based searches (e.g. RPS-Blast) that are known to tolerate much more the "evolution" of functional modules.

Thanks

No competing interests declared.

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Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

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Functional assignment method

Posted by matram on 12 Feb 2012 at 09:51 GMT