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Bioinformatics. 2018 Apr 15;34(8):1414-1415. doi: 10.1093/bioinformatics/btx778.

Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data.

Author information

Bioinformatics Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain.
Departamento de Informática. ESEI-Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas S/N, Universidade de Vigo, 32004 Ourense, Spain.
Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Campus Universitario de Vigo, 36310 Vigo, Spain.
UCIBIO-REQUIMTE, Departamento de Química, Facultade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Lisbon, Portugal.



High-throughput sequencing of bisulfite-converted DNA is a technique used to measure DNA methylation levels. Although a considerable number of computational pipelines have been developed to analyze such data, none of them tackles all the peculiarities of the analysis together, revealing limitations that can force the user to manually perform additional steps needed for a complete processing of the data. This article presents bicycle, an integrated, flexible analysis pipeline for bisulfite sequencing data. Bicycle analyzes whole genome bisulfite sequencing data, targeted bisulfite sequencing data and hydroxymethylation data. To show how bicycle overtakes other available pipelines, we compared them on a defined number of features that are summarized in a table. We also tested bicycle with both simulated and real datasets, to show its level of performance, and compared it to different state-of-the-art methylation analysis pipelines.

Availability and implementation:

Bicycle is publicly available under GNU LGPL v3.0 license at Users can also download a customized Ubuntu LiveCD including bicycle and other bisulfite sequencing data pipelines compared here. In addition, a docker image with bicycle and its dependencies, which allows a straightforward use of bicycle in any platform (e.g. Linux, OS X or Windows), is also available.

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Supplementary information:

Supplementary data are available at Bioinformatics online.

[Indexed for MEDLINE]

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