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Updated: Nov 23, 2025

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Published on: February 1, 2013
CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data
Anna Abramova1,2, Adriana Osińska1,2,3, Haveela Kunche1,2,4
1Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden.
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.
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