Using pseudoalignment and base quality to accurately quantify microbial community composition
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DOI: 10.1371/journal.pcbi.1006096
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- Peter J. Turnbaugh & Micah Hamady & Tanya Yatsunenko & Brandi L. Cantarel & Alexis Duncan & Ruth E. Ley & Mitchell L. Sogin & William J. Jones & Bruce A. Roe & Jason P. Affourtit & Michael Egholm & Be, 2009. "A core gut microbiome in obese and lean twins," Nature, Nature, vol. 457(7228), pages 480-484, January.
- Oren E Livne & Lide Han & Gorka Alkorta-Aranburu & William Wentworth-Sheilds & Mark Abney & Carole Ober & Dan L Nicolae, 2015. "PRIMAL: Fast and Accurate Pedigree-based Imputation from Sequence Data in a Founder Population," PLOS Computational Biology, Public Library of Science, vol. 11(3), pages 1-14, March.
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