De novo motif discovery

This optional workflow discovers enriched sequence motifs from candidate footprint intervals and compares them with known motif databases.

Main commands

call-footprints → discover-motifs → summarize-motifs

First use call-footprints with candidate calling enabled. Then run motif discovery:

discover-motifs --candidates candidate_footprints.bed --genome hg38.fa.gz --flank 75 --method streme \
  --known-motif-db jaspar2026_vertebrates --outdir project/de_novo

summarize-motifs converts MEME/STREME/DREME and Tomtom results into a compact table and optional HTML report.