GenomicTools: a computational platform for developing high-throughput analytics in genomics
GenomicTools: a computational platform for developing high-throughput analytics in genomics
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DOI：
10.1093/bioinformatics/btr646
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发表时间：
2012-01
期刊：
影响因子：
5.8
通讯作者：
Aristotelis Tsirigos;N. Haiminen;Erhan Bilal;F. Utro
中科院分区：
文献类型：
--
作者：
Aristotelis Tsirigos;N. Haiminen;Erhan Bilal;F. Utro
测序技术的最新进展已经导致测序数据的急剧增加，这反过来又需要有效管理计算资源，例如计算时间、存储器要求以及计算管道的原型设计。GenomicTools是一个灵活的计算平台，包括一组命令行工具和一个C++ API，用于分析和操作高通量测序数据，如DNA-seq、RNA-seq、ChIP-seq和MethylC-seq。GenomicTools实现了基因组区域集合之间的各种数学运算，从而实现了计算管道的原型设计，可以解决从预处理和质量控制到荟萃分析的广泛任务。此外，GenomicTools平台旨在通过最小化内存需求来分析任何大小的大型数据集。在实际应用中，在可比的情况下，GenomicTools在时间和内存使用方面优于现有工具。可用性GenomicTools平台（版本2.0.0）是用C++实现的。源代码、文档、用户手册、示例数据集和脚本可在http://code.google.com/p/ibm-cbc-genomic-tools上获得。
MOTIVATION Recent advances in sequencing technology have resulted in the dramatic increase of sequencing data, which, in turn, requires efficient management of computational resources, such as computing time, memory requirements as well as prototyping of computational pipelines. RESULTS We present GenomicTools, a flexible computational platform, comprising both a command-line set of tools and a C++ API, for the analysis and manipulation of high-throughput sequencing data such as DNA-seq, RNA-seq, ChIP-seq and MethylC-seq. GenomicTools implements a variety of mathematical operations between sets of genomic regions thereby enabling the prototyping of computational pipelines that can address a wide spectrum of tasks ranging from pre-processing and quality control to meta-analyses. Additionally, the GenomicTools platform is designed to analyze large datasets of any size by minimizing memory requirements. In practical applications, where comparable, GenomicTools outperforms existing tools in terms of both time and memory usage. AVAILABILITY The GenomicTools platform (version 2.0.0) was implemented in C++. The source code, documentation, user manual, example datasets and scripts are available online at http://code.google.com/p/ibm-cbc-genomic-tools.