SeqLib: a C plus plus API for rapid BAM manipulation, sequence alignment and sequence assembly
SeqLib: a C plus plus API for rapid BAM manipulation, sequence alignment and sequence assembly
复制标题
DOI：
10.1093/bioinformatics/btw741
复制
发表时间：
2017-03-01
期刊：
影响因子：
5.8
通讯作者：
Beroukhim, Rameen
中科院分区：
文献类型：
--
作者：
Wala, Jeremiah;Beroukhim, Rameen
我们推出了 SeqLib，一种 C++ API 和命令行工具，为 BAM/SAM/CRAM 文件、全局序列比对操作和序列组装提供快速且用户友好的界面。四个 C 库在 SeqLib 中执行核心操作：用于 BAM 访问的 HTSlib、用于序列比对的 BWA-MEM 和 BLAT 以及用于纠错和序列组装的 Fermi。基准测试表明，SeqLib 比领先的 C++ 序列分析 API 具有更低的 CPU 和内存要求。我们演示了一个示例，说明最小的 SeqLib 代码如何从 CRAM 文件中提取、纠错和组装读取，然后与 BWA-MEM 对齐。 SeqLib 还提供其他功能，包括染色体感知间隔查询和读取绘图。命令行工具可用于执行集成纠错、微型装配和对准。
We present SeqLib, a C++API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C++sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment.