Department of Computer Science, The University of Texas at Austin, Austin, TX USA, Center for Bioinformatics and Computational Biology, University of Maryland at College Park, College Park, MD USA, Department of Bioengineering, The University of Illinois at Urbana-Champaign, Urbana, IL USA and Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL USA.
Department of Computer Science, The University of Texas at Austin, Austin, TX USA, Center for Bioinformatics and Computational Biology, University of Maryland at College Park, College Park, MD USA, Department of Bioengineering, The University of Illinois at Urbana-Champaign, Urbana, IL USA and Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL USA Department of Computer Science, The University of Texas at Austin, Austin, TX USA, Center for Bioinformatics and Computational Biology, University of Maryland at College Park, College Park, MD USA, Department of Bioengineering, The University of Illinois at Urbana-Champaign, Urbana, IL USA and Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL USA Department of Computer Science, The University of Texas at Austin, Austin, TX USA, Center for Bioinformatics and Computational Biology, University of Maryland at College Park, College Park, MD USA, Department of Bioengineering, The University of Illinois at Urbana-Champaign, Urbana, IL USA and Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL USA.
Bioinformatics. 2014 Dec 15;30(24):3548-55. doi: 10.1093/bioinformatics/btu721. Epub 2014 Oct 29.
Abundance profiling (also called 'phylogenetic profiling') is a crucial step in understanding the diversity of a metagenomic sample, and one of the basic techniques used for this is taxonomic identification of the metagenomic reads.
We present taxon identification and phylogenetic profiling (TIPP), a new marker-based taxon identification and abundance profiling method. TIPP combines SAT'e-enabled phylogenetic placement a phylogenetic placement method, with statistical techniques to control the classification precision and recall, and results in improved abundance profiles. TIPP is highly accurate even in the presence of high indel errors and novel genomes, and matches or improves on previous approaches, including NBC, mOTU, PhymmBL, MetaPhyler and MetaPhlAn.
丰度剖析（也称为“系统发育剖析”）是理解宏基因组样本多样性的关键步骤，用于此的基本技术之一是对宏基因组读取进行分类鉴定。
我们提出了基于标记的分类鉴定和丰度剖析（TIPP），这是一种新的基于标记的分类鉴定和丰度剖析方法。TIPP 结合了 SAT 启用的系统发育定位方法，以及用于控制分类精度和召回率的统计技术，从而生成改进的丰度剖析结果。TIPP 即使在存在高插入缺失错误和新基因组的情况下也具有高度准确性，并且与包括 NBC、mOTU、PhymmBL、MetaPhyler 和 MetaPhlAn 在内的先前方法相匹配或改进。
