loreme 0.1.1

Extract Methylation calls from ONT or PB long read data

LoReMe pipeline

TODO: make a 'loreme clean' subcommand to remove downloads before uninstalling

LoReMe (Long Read Methylaton) is a Python package facilitating analysis of DNA methylation signals from Pacific Biosciences or Oxford Nanopore long read sequencing data.

It consists of an API and CLI for three distinct applications:

1. Pacific Biosciences data processing. PB reads in SAM/BAM format are aligned to a reference genome with the special-purpose aligner pbmm2, a modified version of minimap2. Methylation calls are then extracted from the aligned reads by pb-CpG-tools.

2. Oxford nanopore basecalling. ONT reads are optionally converted from FAST5 to POD5 format, then basecalled and aligned to a reference with dorado. (dorado alignment also uses minimap2 under the hood).

3. Postprocessing and QC of methylation calls. Several functions are available to generate diagnostic statistics and plots.

See also the full documentation.

Other tools of interest: methylartist and modbamtools (modbamtools docs), methplotlib

Installation

Conda

The recommended way to install loreme is with a dedicated conda environment:

First create an environment including all dependencies:

conda create -n loreme -c conda-forge -c bioconda pbmm2 urllib3 \
  pybedtools gff2bed seaborn pyfaidx psutil gputil tabulate \
  cython h5py iso8601 more-itertools polars tqdm
conda activate loreme

Then install with pip:

pip install loreme

Alternatively, install from the git repo:

git clone https://gitlab.com/salk-tm/loreme.git
cd loreme
pip install .

You may also wish to install nvtop to monitor GPU usage:

conda install -c conda-forge nvtop

Check installation

Check that the correct version was installed with loreme --version