BFC：校正Illumina测序错误。
BFC: correcting Illumina sequencing errors.
作者信息
Li Heng
机构信息
Medical Population Genetics Program, Broad Institute, Cambridge, MA 02142, USA.
出版信息
Bioinformatics. 2015 Sep 1;31(17):2885-7. doi: 10.1093/bioinformatics/btv290. Epub 2015 May 6.
Abstract
UNLABELLED
BFC is a free, fast and easy-to-use sequencing error corrector designed for Illumina short reads. It uses a non-greedy algorithm but still maintains a speed comparable to implementations based on greedy methods. In evaluations on real data, BFC appears to correct more errors with fewer overcorrections in comparison to existing tools. It particularly does well in suppressing systematic sequencing errors, which helps to improve the base accuracy of de novo assemblies.
AVAILABILITY AND IMPLEMENTATION
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
未标注
BFC是一款免费、快速且易于使用的测序错误校正工具，专为Illumina短读长序列设计。它采用非贪婪算法，但仍保持与基于贪婪方法的实现相当的速度。在对真实数据的评估中，与现有工具相比，BFC似乎能以更少的过度校正纠正更多错误。它在抑制系统性测序错误方面表现尤其出色，这有助于提高从头组装的碱基准确性。
可用性及实现方式
联系方式
补充信息
补充数据可在《生物信息学》在线获取。
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Genome Biol. 2014;15(11):509. doi: 10.1186/s13059-014-0509-9.
3
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