CAFE：用于分析配对样本转座子插入测序数据的软件套件。
CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data.
作者信息
Abramova Anna, Osińska Adriana, Kunche Haveela, Burman Emil, Bengtsson-Palme Johan
机构信息
Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden.
Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, SE- 40530 Gothenburg, Sweden.
出版信息
Bioinformatics. 2021 Apr 9;37(1):121-122. doi: 10.1093/bioinformatics/btaa1086.
SUMMARY
Sequencing of transposon insertion libraries is used to determine the relative fitness of individual mutants at a large scale. However, there is a lack of tools for specifically analyzing data from such experiments with paired sample designs. Here, we introduce CAFE-Coefficient-based Analysis of Fitness by read Enrichment-a software package that can analyze data from paired transposon mutant sequencing experiments, generate fitness coefficients for each gene and condition and perform appropriate statistical testing on these fitness coefficients.
AVAILABILITY AND IMPLEMENTATION
CAFE is implemented in Perl and R. The source code is freely available for download under the MIT License from https://github.com/bengtssonpalme/cafe and http://microbiology.se/software/cafe/.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
转座子插入文库测序用于大规模确定单个突变体的相对适应性。然而，缺乏专门用于分析此类配对样本设计实验数据的工具。在此，我们引入了基于CAFE系数的富集读数适应性分析——一个软件包，它可以分析来自配对转座子突变体测序实验的数据，为每个基因和条件生成适应性系数，并对这些适应性系数进行适当的统计测试。
可用性和实现方式
CAFE用Perl和R语言实现。源代码可根据麻省理工学院许可从https://github.com/bengtssonpalme/cafe和http://microbiology.se/software/cafe/免费下载。
补充信息
补充数据可在《生物信息学》在线获取。
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