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Open Access Highly Accessed Research article

Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows

Jorge Barriuso, Jose R Valverde and Rafael P Mellado*

Author Affiliations

Centro Nacional de Biotecnología (CSIC), c/Darwin 3, 28049 Madrid, Spain

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BMC Bioinformatics 2011, 12:473  doi:10.1186/1471-2105-12-473

Published: 14 December 2011

Additional files

Additional file 1:

Table S1.1 OTU counts. J-C: Jukes-Cantor; 50 × 60 seq mut inter: 50 mutated copies of the 60 sequences dataset interleaved; 50 × 60 seq mut stack: 50 mutated copies of the 60 sequences dataset stacked; NC: not computable; t1, t2: samples taken at time 1 or time 2 (see Methods). Values marked with an * were computed using only unique sequences. Table S1.2 ACE estimates J-C: Jukes-Cantor; 50 × 60 seq mut inter: 50 mutated copies of the 60 sequences dataset interleaved; 50 × 60 seq mut stack: 50 mutated copies of the 60 sequences dataset stacked; NC: not computable; t1, t2: samples taken at time 1 or time 2 (see Methods). Values marked with an * were computed using only unique sequences. CROP, Outpipe and RDP does not compute the ACE estimator. Table S1.3 Chao1 estimates J-C: Jukes-Cantor; 50 × 60 seq mut inter: 50 mutated copies of the 60 sequences dataset interleaved; 50 × 60 seq mut stack: 50 mutated copies of the 60 sequences dataset stacked; NC: not computable; t1, t2: samples taken at time 1 or time 2 (see Methods). Values marked with an * were computed using only unique sequences. CROP and Outpipe does not compute the Chao1 estimator.

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Additional file 2:

Table S2. Computational time needed for each step in the diversity analysis. J-C: Jukes-Cantor. Time is indicated as hours: minutes: seconds. *Alignment was calculated using -maxiter 2.

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Open Data

Additional file 3:

This file contains the FASTA formatted sequences of all the datasets used in this study. Zip file contents are briefly described in the included README file.

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Open Data