Open Access Highly Accessed Research article

Sequencing platform and library preparation choices impact viral metagenomes

Sergei A Solonenko1, J César Ignacio-Espinoza2, Adriana Alberti3, Corinne Cruaud3, Steven Hallam4, Kostas Konstantinidis5, Gene Tyson6, Patrick Wincker3 and Matthew B Sullivan12*

Author Affiliations

1 Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA

2 Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA

3 CEA, DSV, IG, Genoscope, 2 rue Gaston Crémieux CP5706, Evry, Cedex, 91057, France

4 Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada

5 Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA

6 Austalian Center for Ecogenomics, University of Queensland, Brisbane, QLD, Australia

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BMC Genomics 2013, 14:320  doi:10.1186/1471-2164-14-320

Published: 10 May 2013

Additional files

Additional file 1: Figures S1-S11:

A log-log plot of all B2 Ocean metagenome read yields per starting DNA amount (Figure S1). % G + C histogram of several ‘problematic’ and ‘reliable’ libraries, and GC distribution of full dsDNA bacteriophage genomes for reference (Figure S2). %G + C distribution differences between whole-read mean % G + C in unamplified 454 metagenome, in green, and Sanger-sequenced fosmid library, in blue, shows a shift toward high %G + C in the fosmid library (Figure S3). Duplicate frequencies in Experiment 1 metagenomes (Figure S4). Heatmap of Pearson’s r pairwise correlation values for artificial duplicate frequencies, as detected using CD-HIT-454 for 454 and Ion Torrent data and CD-HIT-DUP for Illumina data (Figure S5). CD-HIT-454 artificial duplicate frequencies in Experiment 1 metagenomes generated using 454 and Ion Torrent sequencing (Figure S6). Duplicate frequency minus artificial duplicate frequency for Experiment 1 CD-HIT-454 –processed metagenomes (Figure S7). CD-HIT-DUP artificial duplicate frequencies in Experiment 1 Illumina metagenomes (Figure S8). Duplicate frequency minus artificial duplicate frequency for Experiment 1 CD-HIT-DUP –processed metagenomes (Figure S9). Ion Torrent QC length distribution (Figure S10). Methods for Trimming Illumina Reads (Figure S11).

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Additional file 2:

Pyrotag data for microbial composition of Biosphere 2 Ocean in Nov 2008 and Sep 2009. The Biosphere 2 Ocean was the source of the DNA sample used in Experiment 1 metagenomes. The distribution of microbial phyla in the B2 Ocean community appears stable across two samples taken a year apart.

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