Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method

September 2012

Melissa B. Duhaime, Li Deng, Bonnie T. Poulos, and Matthew B. Sullivan

A study of most reproducible and sample-efficient methods for sequencing meta-genomic samples with very low abundance samples (20 L ocean water ->1 pg to 1 ng DNA). Detailed side-by-side comparison of standard gel isolation, Pippin Prep, and AMPure bead size selections. The Pippin Prep demonstrated the superior efficiency and reproducibility. Materials and methods: Covaris shearing, end-repair and adapter addition, Pippin size-fractionation, enrichment amplification, sequencing (on 454GLX or Illumina Hi-Seq).

Environmental Microbiology (2012) 14(9), 2526–2537

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