BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data
BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data
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BioKIT：用于处理和分析不同类型序列数据的多功能工具包
DOI：
10.1093/genetics/iyac079
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发表时间：
2022
期刊：
影响因子：
3.3
通讯作者：
Hadjifrangiskou, Maria
中科院分区：
文献类型：
--
作者：
Steenwyk, Jacob L;Buida, Thomas J;Gonçalves, Carla;Goltz, Dayna C;Morales, Grace;Mead, Matthew E;LaBella, Abigail L;Chavez, Christina M;Schmitz, Jonathan E;Hadjifrangiskou, Maria
生物信息学分析--如基因组组装质量评估、比对汇总统计、相对同义密码子使用、文件格式转换以及处理和分析--被纳入生物科学的不同学科。已经开发了几个命令行软件来进行其中一些单独的分析，但缺乏进行所有这些分析的统一工具包。为了弥补这一差距，我们引入了Biokit，这是一个多功能的命令行工具包，一旦发布，它就有42个功能，其中几个是社区来源的，用于对基因组组合、多序列比对、编码序列、测序数据等进行常规和新颖的处理和分析。为了证明Biokit的实用性，我们对171个使用替代遗传密码的真菌基因组的相对同义密码子使用进行了全面的检查，结果表明，新的基因相对同义密码子使用指标可以准确地估计基因方面的密码子优化，评估901个真核基因组组合的质量和特征，并计算10个系统基因组数据矩阵的比对汇总统计数据。Biokit将有助于促进和简化序列分析工作流程。Biokit根据麻省理工学院的许可从GitHub(https://github.com/JLSteenwyk/BioKIT)，PYPI(https://pypi.org/project/jlsteenwyk-biokit/)，和蟒蛇云(https://anaconda.org/jlsteenwyk/jlsteenwyk-biokit).)免费获得有关请求新功能的文档、用户教程和说明，可在线获取(https://jlsteenwyk.com/BioKIT).
Bioinformatic analysis—such as genome assembly quality assessment, alignment summary statistics, relative synonymous codon usage, file format conversion, and processing and analysis—is integrated into diverse disciplines in the biological sciences. Several command-line pieces of software have been developed to conduct some of these individual analyses, but unified toolkits that conduct all these analyses are lacking. To address this gap, we introduce BioKIT, a versatile command line toolkit that has, upon publication, 42 functions, several of which were community-sourced, that conduct routine and novel processing and analysis of genome assemblies, multiple sequence alignments, coding sequences, sequencing data, and more. To demonstrate the utility of BioKIT, we conducted a comprehensive examination of relative synonymous codon usage across 171 fungal genomes that use alternative genetic codes, showed that the novel metric of gene-wise relative synonymous codon usage can accurately estimate gene-wise codon optimization, evaluated the quality and characteristics of 901 eukaryotic genome assemblies, and calculated alignment summary statistics for 10 phylogenomic data matrices. BioKIT will be helpful in facilitating and streamlining sequence analysis workflows. BioKIT is freely available under the MIT license from GitHub (https://github.com/JLSteenwyk/BioKIT), PyPi (https://pypi.org/project/jlsteenwyk-biokit/), and the Anaconda Cloud (https://anaconda.org/jlsteenwyk/jlsteenwyk-biokit). Documentation, user tutorials, and instructions for requesting new features are available online (https://jlsteenwyk.com/BioKIT).
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影响因子：
2.7
作者：
Borowiec ML
通讯作者：
Borowiec ML
影响因子：
10.7
作者：
Kumar, Sudhir;Stecher, Glen;Tamura, Koichiro
通讯作者：
Tamura, Koichiro
影响因子：
13.6
作者：
Shen XX;Steenwyk JL;LaBella AL;Opulente DA;Zhou X;Kominek J;Li Y;Groenewald M;Hittinger CT;Rokas A
通讯作者：
Rokas A
DOI：
10.1073/pnas.95.11.5906
发表时间：
1998-05-26
影响因子：
11.1
作者：
Britten, RJ
通讯作者：
Britten, RJ
DOI：
10.1073/pnas.84.13.4355
发表时间：
1987-07-01
影响因子：
11.1
作者：
GRIBSKOV, M;MCLACHLAN, AD;EISENBERG, D
通讯作者：
EISENBERG, D