UCHIME improves sensitivity and speed of chimera detection.
UCHIME improves sensitivity and speed of chimera detection.
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DOI：
10.1093/bioinformatics/btr381
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发表时间：
2011-08-15
期刊：
影响因子：
--
通讯作者：
Knight R
中科院分区：
文献类型：
--
作者：
Edgar RC;Haas BJ;Clemente JC;Quince C;Knight R
动机：嵌合DNA序列通常在聚合酶链反应扩增过程中形成，特别是当对单个区域（例如16S rRNA或真菌内转录间隔区）进行测序以评估多样性或比较种群时。未被发现的嵌合体可能被误解为新物种，导致对多样性的夸大估计和对种群之间差异的虚假推断。因此，嵌合体的检测和去除在此类实验中至关重要。结果：我们描述了UCHIME，一个新的程序，检测嵌合序列的两个或多个部分。UCHIME要么使用无嵌合体序列的数据库，要么通过利用丰度数据来检测新的嵌合体。UCHIME比ChimeraSlayer（以前最敏感的数据库方法）具有更好的灵敏度，特别是对于短的噪声序列。在对具有已知组成的人工细菌群落的测试中，显示UCHIME从头敏感性与Perseus相当。UCHIME比Perseus快100倍，比ChimeraSlayer快1000倍。联系方式：robert@drive5.com可用性：来源、二进制文件和数据：http://drive5.com/uchime。补充信息：补充数据可在Bioinformatics在线获得。
Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments. Results: We describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer. Contact: robert@drive5.com Availability: Source, binaries and data: http://drive5.com/uchime. Supplementary information: Supplementary data are available at Bioinformatics online.
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