Thus, wg-blimp is a relevant alternative to previous analysis pipelines and may facilitate future epigenetic research. We demonstrated its applicability by analysing multiple publicly available datasets. Wg-blimp provides a comprehensive analysis pipeline for whole genome bisulfite sequencing data as well as a user interface for simplified result inspection. Segmentation results were consistent with previous analyses, despite different reference genomes and sequencing techniques. As expected, unmethylated regions were in close proximity of transcription start sites. We further applied wg-blimp to a publicly available sample of embryonic stem cells to showcase methylome segmentation. We were able to replicate 112 of 114 previously published regions, and found results to be consistent with previous findings. To demonstrate wg-blimp’s ability to produce correct results we used it to call differentially methylated regions for two publicly available datasets. We improve on previous pipelines by providing a more comprehensive analysis workflow as well as an interactive user interface. Comparing wg-blimp to previous end-to-end pipelines reveals similar setups for common sequence processing tasks, but shows differences for post-alignment analyses. It integrates established algorithms for alignment, quality control, methylation calling, detection of differentially methylated regions, and methylome segmentation, requiring only a reference genome and raw sequencing data as input. We developed wg-blimp ( whole genome bisu lf ite sequencing methylation analysis pipeline) as an end-to-end pipeline to ease whole genome bisulfite sequencing data analysis. Furthermore, previous pipelines lack features or show technical deficiencies, thus impeding analyses. While many algorithms have been developed for tasks such as alignment, comprehensive end-to-end pipelines are still sparse. Analysing whole genome bisulfite sequencing datasets is a data-intensive task that requires comprehensive and reproducible workflows to generate valid results.
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