A novel and well-defined benchmarking method for second generation read mapping.
A novel and well-defined benchmarking method for second generation read mapping.
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DOI：
10.1186/1471-2105-12-210
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发表时间：
2011-05-26
影响因子：
3
通讯作者：
Reinert K
中科院分区：
文献类型：
--
作者：
Holtgrewe M;Emde AK;Weese D;Reinert K
第二代测序技术以超高通量产生DNA序列数据。大多数生物学应用的共同点是将读数映射到几乎相同或高度相似的参考基因组。读取映射结果质量的评估并不简单，迄今为止尚未正式化。因此，以统一的方式比较不同的读取映射方法并确定哪个程序最适合什么任务并不容易。我们提出了一个新的基准方法，称为Rabema（读对齐BEnchMArk），读映射。它由读映射问题的严格定义和用于评估支持SAM输出格式的任意读映射器的结果的工具组成。我们通过比较流行的读取映射器来展示基准程序的有用性。支持基准测试的工具是在GPL下许可的，可以从http://www.seqan.de/projects/rabema.html获得。
Second generation sequencing technologies yield DNA sequence data at ultra high-throughput. Common to most biological applications is a mapping of the reads to an almost identical or highly similar reference genome. The assessment of the quality of read mapping results is not straightforward and has not been formalized so far. Hence, it has not been easy to compare different read mapping approaches in a unified way and to determine which program is the best for what task. We present a new benchmark method, called Rabema (Read Alignment BEnchMArk), for read mappers. It consists of a strict definition of the read mapping problem and of tools to evaluate the result of arbitrary read mappers supporting the SAM output format. We show the usefulness of the benchmark program by performing a comparison of popular read mappers. The tools supporting the benchmark are licensed under the GPL and available from http://www.seqan.de/projects/rabema.html.