methdb 0.0.2

mdb: population-level DNA methylation analysis toolkit

mdb

A toolkit to create DNA methylation database for cross-sample comparison

Requirement

Output format taken from:

• Modkit >= v0.6
• Pb-CpG-tools >= v3.0.0

Recommended DNA methylation pileup parameter:

• Use --combine-strand in modkit pileup.
• Use -m function to aggregrate 5mC and 5hmC for ONT's pileup if merging ONT with PacBio.

mdb features

• mdb creates a genome-wide CpG matrix to support massive computing with population-level DNA methylation signals

• Use mdb index to index reference genome

• Use mdb create to create .mdb files (a set of .npy files) for each methylBED file

• Use mdb merge to merge per sample .mdb database to form a CpGxSample matrix

• Use mdb pca to parform PCA on merged matrix

    usage: mdb [-h] [-v] {index,create,merge,pca} ...
  
    DNA methylation database builder for quick population-level analysis.
  
    positional arguments:
    {index,create,merge,pca}
        index               Index all CpG locations on the reference genome
        create              Create single sample-level methylation database
        merge               mdb databases from multiple samples into a single database: COMBINE STRAND and HAPLOTYPE
        pca                 Perform PCA on the merged mdb database
  
    options:
    -h, --help            show this help message and exit
    -v, --version         show program's version number and exit
  
    Version v0.0.2