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Panmethyl

Panmethyl is a nextflow pipeline that maps epigenetic data from long-reads to pangenomes.

Apptainer image

apptainer pull --arch amd64 panmethyl.sif library://cgroza/collection/panmethyl:latest

Inputs

It takes the following inputs:

  • --out - directory in which panmethyl will write the output files.
  • --bams - CSV file listing the BAM files to be mapped to the pangenome.

The format of this CSV file is:

sample,path
name1,path/to/bam1
name2,path/to/bam2

These BAM files must be annotated with the appropriate epigenetic information. For example, the location of modified bases must be encoded in the MM tag and the likelihoods of modification must be encoded in the ML tag.

  • --graph - Pangenome in GFA format.
  • --lift - Lift nucleotide positions from graph coordinates to path (assembly) coordinates. Assumes GFA with P lines. Useful for generating frequency distributions.
  • --bed - BED file enumerating the intervals over which to summarize modification levels. Intervals must be in path (assembly) coordinates.
  • --aligner - Choose which aligner will map the reads to the graph. Possibilities are `minigraph` and `GraphAligner`.
  • --code - Modification code in hte MM/ML tags, according to the SAM spec. For example, C+m.
  • --motif - Nucleotides (or dinucleotides) targeted by the modification. Possible values are A, T, G, C, CG.

Outputs

Panmethyl outputs a CSV plain text file for each entry in --bams. This file is a CSV file listing the graph node, the position of the modified base, its strand, the coverage on the modified base, and the average methylation level, encoded on a scale from 0 to 255 (as in the ML tag).

Citation

If using panmethyl, please cite:

  • Groza, C., Ge, B., Cheung, W. A., Pastinen, T., & Bourque, G. (2025). Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA. Genome research, 35(4), 644–652. https://doi.org/10.1101/gr.279240.124