论文标题
基因组：指尖的基因和基因组
genomepy: genes and genomes at your fingertips
论文作者
论文摘要
分析功能性基因组学实验，例如ATAC-，芯片或RNA序列，需要参考参数，包括基因组组装和基因注释。这些资源通常可以从不同的组织和不同版本中检索。大多数生物信息学工作流程都要求用户手动提供此基因组数据，这可能是一个乏味且容易出错的过程。 在这里，我们提出基因组，可以搜索，下载和预处理正确的基因组数据以进行分析。基因组可以搜索NCBI，ENSEMBL，UCSC和GENCODE的基因组数据，并比较可用的基因注释以实现知情决定。可以通过明智但可控制的默认值下载和预处理所选的基因组和基因注释。可以自动生成或下载其他支持数据，例如对准器索引，基因组元数据和黑名单。 https://github.com/vanheeringen-lab/genomepy在MIT许可下免费获得Genomepy，可以通过PIP或Bioconda安装。
Analyzing a functional genomics experiment, such as ATAC-, ChIP- or RNA-sequencing, requires reference data including a genome assembly and gene annotation. These resources can generally be retrieved from different organizations and in different versions. Most bioinformatic workflows require the user to supply this genomic data manually, which can be a tedious and error-prone process. Here we present genomepy, which can search, download, and preprocess the right genomic data for your analysis. Genomepy can search genomic data on NCBI, Ensembl, UCSC and GENCODE, and compare available gene annotations to enable an informed decision. The selected genome and gene annotation can be downloaded and preprocessed with sensible, yet controllable, defaults. Additional supporting data can be automatically generated or downloaded, such as aligner indexes, genome metadata and blacklists. Genomepy is freely available at https://github.com/vanheeringen-lab/genomepy under the MIT license and can be installed through pip or bioconda.
