Methplotlib Analysis of modified nucleotides from nanopore sequencing
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Visualisation of modified nucleotides
The presence of covalent nucleotide modifications such as methylcytosine can be detected directly from the Oxford Nanopore Technologies sequencers MinION or PromethION, as these marks will affect the current signal. We have developed methplotlib, software for the quality control, visualization and further processing of nucleotide modifications, compatible with nanopolish, nanocompore and direct methylation calling using the Guppy basecaller, compatible with MM and MP tags in CRAM format. The plots are in dynamic HTML enabling zooming and selection of the most interesting part of the visualization. The visualizations can be made for multiple samples and contain the modified frequency or the raw per read per position probabilities of modifications, together with annotations in GTF and BED format on gene structure and e.g. CpG islands or other regulatory features.