SimLoRD：长读长数据模拟
SimLoRD: Simulation of Long Read Data.
作者信息
Stöcker Bianca K, Köster Johannes, Rahmann Sven
机构信息
Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, Essen, 45147, Germany.
Life Sciences, Centrum Wiskunde & Informatica (CWI), Amsterdam 1098 XG, The Netherlands Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
出版信息
Bioinformatics. 2016 Sep 1;32(17):2704-6. doi: 10.1093/bioinformatics/btw286. Epub 2016 May 10.
MOTIVATION
Third generation sequencing methods provide longer reads than second generation methods and have distinct error characteristics. While there exist many read simulators for second generation data, there is a very limited choice for third generation data.
RESULTS
We analyzed public data from Pacific Biosciences (PacBio) SMRT sequencing, developed an error model and implemented it in a new read simulator called SimLoRD. It offers options to choose the read length distribution and to model error probabilities depending on the number of passes through the sequencer. The new error model makes SimLoRD the most realistic SMRT read simulator available.
AVAILABILITY AND IMPLEMENTATION
SimLoRD is available open source at http://bitbucket.org/genomeinformatics/simlord/ and installable via Bioconda (http://bioconda.github.io).
CONTACT
Bianca.Stoecker@uni-due.de or Sven.Rahmann@uni-due.de
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
第三代测序方法提供的读长比第二代方法更长，且具有独特的错误特征。虽然存在许多用于第二代数据的读段模拟器，但用于第三代数据的选择非常有限。
结果
我们分析了来自太平洋生物科学公司（PacBio）单分子实时（SMRT）测序的公共数据，开发了一个错误模型，并在一个名为SimLoRD的新读段模拟器中实现了该模型。它提供了选择读长分布以及根据通过测序仪的次数对错误概率进行建模的选项。新的错误模型使SimLoRD成为现有的最逼真的SMRT读段模拟器。
可用性和实现方式
SimLoRD可在http://bitbucket.org/genomeinformatics/simlord/上开源获取，并可通过Bioconda（http://bioconda.github.io）进行安装。
联系方式
Bianca.Stoecker@uni-due.de或Sven.Rahmann@uni-due.de
补充信息
补充数据可在《生物信息学》在线版获取。
Zotero 插件