wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data

Abstract

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

MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant WGBS data

“…MethylScore is designed as a post-alignment, secondary analysis workflow starting from either alignments in bam format or pre-existing single-cytosine metrics in bedGraph format, in contrast to existing end-to-end solutions such as wg-blimp (Wöste et al, 2020) or PiGx bsseq (Wurmus et al, 2018). However, its modular design also allows for tight integration with primary analysis pipelines such as nf-core methylseq (Ewels et al, 2020), snakePipes WGBS (Bhardwaj et al, 2019), or EpiDiverse Toolkit (Nunn et al, 2021).…”

msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data

“…msPIPE and similar pipelines for methylation analysis [ 26 , 33 – 37 , 46 , 47 ] were compared in terms of installation, supported sub-steps, downstream analyses, and the difficulty of setting a reference (Table 1 ). Most of them can be easily installed by using a cross-platform and dependency-free package manager, such as Docker and Bioconda.…”

“…MultiQC Bismark methylKit methylKit NA NA Manual snakePipes [ 46 ] Bioconda Cutadapt Trim Galore! Fastp MultiQC bwa-meth MethylDackel dmrseq DSS metilene NA NA Partially automatic c wg-blimp [ 47 ] Bioconda Docker MultiQC bwa-meth MethylDackel bsseq camel metilene MethylSeekR NA Manual NA not available a All required files of a reference can be automatically prepared and set if the data exists in the UCSC Genome Browser database [ 40 ], and manual setting is also supported b All required files of a reference can be automatically prepared and set if the data exists in the iGenomes database [ 48 ], and manual setting is also supported c All required files of a reference can be automatically prepared and set if the reference is one of five species (human, mouse, zebrafish, fruit fly, and fission yeast), and manual setting is also supported …”

Accelerating the Alignment Processing Speed of the Comprehensive End-to-End Whole-Genome Bisulfite Sequencing Pipeline, wg-blimp

“…1). To accomplish this, we rst determined the runtime required for alignment by each pipeline using existing small sample datasets provided to test the wg-blimp pipeline installation, which included isogenic human blood and sperm WGBS sequencing les (each generated from pools of DNA from six men) with nearly 1M reads each, all restricted to chr22 [12,19]. We found the relative alignment speed was similar for both bwa-meth and gemBS with the average bwa-meth alignment time being only slightly shorter than the gemBS alignment time.…”

“…Recently, a novel snakemake [11] work ow termed wg-blimp was described as an "end-to-end" pipeline for processing WGBS data by integrating established algorithms for alignment, quality control (QC), methylation calling, detection of differentially methylated regions (DMRs), and methylation segmentation for pro ling of DNA methylation states at regulatory elements [12]. The wg-blimp pipeline is simple to install on either a personal computer or in a research high computing cluster, often requiring only an input reference, gene annotation, and FASTQ read les to fully process WGBS data.…”