File Types

GFA: Graphical Fragment Assembly format

For detail explanation, refer to https://gfa-spec.github.io/GFA-spec/GFA1.html

GAF: Graphical mApping Format

For detail explanation, refer to https://github.com/lh3/gfatools/blob/master/doc/rGFA.md

methyl: Graph methylation file

The methylGrapher extraction output provides a list of each cytosine mapped to the genome graph, specified by its coordinates (segment ID, 0-based position on the segment, and strand relative to the segment). For each cytosine, the output includes its context, the number of read-pairs supporting whether the cytosine is methylated or unmethylated, and the coverage, which is the sum of methylated and unmethylated read-pairs. The methylation percentage is calculated as the ratio of methylated read-pairs to the total coverage.

Reference:

1. The design and construction of reference pangenome graphs with minigraph

2. Glossary of vg-related File Types