Abstract
The updated release of ‘NGSmethDB’ (http://bioinfo2.ugr.es/NGSmethDB) is a repository for single-base whole-genome methylome maps for the best-assembled eukaryotic genomes. Short-read data sets from NGS bisulfite-sequencing projects of cell lines, fresh and pathological tissues are first pre-processed and aligned to the corresponding reference genome, and then the cytosine methylation levels are profiled. One major improvement is the application of a unique bioinformatics protocol to all data sets, thereby assuring the comparability of all values with each other. We implemented stringent quality controls to minimize important error sources, such as sequencing errors, bisulfite failures, clonal reads or single nucleotide variants (SNVs). This leads to reliable and high-quality methylomes, all obtained under uniform settings. Another significant improvement is the detection in parallel of SNVs, which might be crucial for many downstream analyses (e.g. SNVs and differential-methylation relationships). A next-generation methylation browser allows fast and smooth scrolling and zooming, thus speeding data download/upload, at the same time requiring fewer server resources. Several data mining tools allow the comparison/retrieval of methylation levels in different tissues or genome regions. NGSmethDB methylomes are also available as native tracks through a UCSC hub, which allows comparison with a wide range of third-party annotations, in particular phenotype or disease annotations.
Highlights
DNA methylation is an epigenome mark involved in key biological processes [1,2,3], such as embryonic development, transcription, genomic imprinting, learning, memory or age-related cognitive decline [4,5,6,7]
We made NGSmethDB methylation maps directly available through a UCSC track hub, a web-accessible directory of genomic data that can be viewed on the UCSC genome browser
All methylome maps stored in the database were obtained under uniform conditions, i.e. using strictly the same bioinformatics protocol for all raw data sets including the same parameter settings and the same stringent quality controls
Summary
DNA methylation is an epigenome mark involved in key biological processes [1,2,3], such as embryonic development, transcription, genomic imprinting, learning, memory or age-related cognitive decline [4,5,6,7]. A wide variety of methodologies to pre-process the data, aligning the reads or inferring the methylation states has been used in compiling these databases, leading to methylomes obtained with very different methods or parameter sets to be included into the same database, which can bias downstream analyses. An updated list of the data sets used for each genome, with detailed information on the source cell-line or tissue, is maintained online (http:// bioinfo2.ugr.es/NGSmethDB/database.php). Methylation maps for minimum coverages of 1, 3, 5 or 10 reads (http://bioinfo2.ugr.es/NGSmethDB/database.php) were generated. The user interface was improved by replacing ‘Gbrowse’ with ‘Jbrowse’ [40,41], resulting in a methylation browser with a fast and smooth scrolling and zooming mechanism (Figure 2) This speeds data download and upload, and requires light server resources. A general and context-dependent help about searching, moving, zooming and showing/hiding tracks with JBrowse has been interactively integrated in the proper methylation browser window
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