Methylome segmentation algorithm using a changepoint detection HMM
Project description
NanoEpiSeg 1.0.0b1
NanoEpiSeg is a tool for de novo segmentation of a methylome from read-level methylation calls (such as Nanopolish).
NanoEpiSeg is currently in development. Please do not hesitate to report bugs or feature requests.
A detailed documentation is in the works, stay tuned!
Prerequisites
NanoEpiSeg assumes that your methylation calls are stored in MetH5 format.
Installation
Through pip:
pip install nanoepiseg
Through anaconda:
conda install -c snajder-r nanoepiseg
Usage
NanoEpiSeg is meant to be parallelizable, which is why you would typically call nanoepiseg on a cluster system in parallel. In order to best accomplish load-balancing, it is done per hdf5 chunk.
You can list the number of chunks per chromosome via:
nanoepiseg list_chunks --m5file INPUT_FILE.m5
To then perform segmentation for a certain chunk, you can run:
nanoepiseg segment_h5 --m5file INPUT_FILE.m5 \
--out_tsv OUTPUT_FILE \
--reader_workers NUM_READER_WORKERS \
--workers NUM_SEGMENTATION_WORKERS \
--chromosome CHROMOSOME \
--chunks CHUNK1 [CHUNK2 ...]
There are further options available. Please check out the help to discover them.
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