nanodisco documentation¶
nanodisco is a toolbox for de novo discovery of all the three types (6mA, 5mC and 4mC) of DNA methylation from individual bacteria and microbiomes using nanopore sequencing. For microbiomes, nanodisco also supports the use of DNA methylation patterns as natural epigenetic barcodes to facilitate high resolution metagenomic binning.
Features¶
- De novo discover DNA methylation motifs, identify specific type (6mA, 5mC or 4mC, namely typing) of a methylation motif, and identify which specific position within the motif is methylated (namely fine mapping).
- Perform metagenomic binning based on microbial DNA methylation pattern by constructing and clustering a methylation profile matrix.
- Integrate the two functionalities above together for de novo methylation motif discovery from microbiomes, and metagenomic analysis.
Authors’ notes¶
We are actively developing nanodisco to facilitate usage and broaden features. All feedback is more than welcome. You can reach us on twitter (@iamfanggang and @AlanTourancheau) or directly through the GitHub issues system.
Installation¶
nanodisco is distributed as a fully functional image, bypassing the need to install any dependencies others than the virtualization software. We currently recommend using Singularity (v3.2.1 and above), which can be installed on Linux systems and is often the preferred solution by HPC administrators (Quick Start). nanodisco was tested extensively with Singularity v3.2.1 and v3.5.2.
singularity pull --name nanodisco.sif library://fanglab/default/nanodisco # Download the image from cloud.sylabs.io
singularity build nd_env nanodisco.sif # Create a container named nd_env