mBin overview

mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads

The mBin pipeline is designed to discover the unique signals of DNA methylation in metagenomic SMRT sequencing reads and leverage them for organism binning of assembled contigs or unassembled reads. Because all cellular DNA is modified by the same set of methyltransferases encoded in the genome, DNA methylation signals can be used for binning not just chromosomal sequences, but also extrachromosomal mobile genetic elements like plasmids.

The pipeline consists of four routines:

1. buildcontrols: Gets unmethylated IPD values for motifs from whole-genome amplified (WGA) sequencing
2. filtermotifs: Identifies methylated motifs in native metagenomic sequencing
3. methylprofiles: Creates methylation profiles for sequences using specified motifs
4. mapfeatures: Visualizes landscape of methylation features across all sequences

Please note: mbin was initially developed for PacBio RS II data. Currently it does not support bam files in the Sequel system yet. We do plan to support Sequel data in the near future, and will make sure update this page as soon as an update is available.

Documentation

For a comprehensive guide on how to install and run mBin, please see the full documentation.

Citations

Beaulaurier J, Zhu S, Deikus G, Mogno I, Zhang XS, Davis-Richardson A, Canepa R, Triplett E, Faith J, Sebra R, Schadt EE, Fang G. Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nature Biotechnology 36, 61-69 (2018). doi:10.1038/nbt.4037.

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.