SWARM user guide

Use SWARM to detect and analyse m6A, Ψ, and m5C from nanopore data.

My plot

Features

  • SWARM_read_level.py - Detect modifications at each base in individual reads.

  • SWARM_site_level.py - Measure modification status at reference coordinates.

  • SWARM_diff.py - Identify modified sites which vary between conditions.

Required inputs

.fasta file     # Reference transcriptome. *Genome alignment possible with workarounds.
.blow5 file     # Contains easily accessible raw nanopore signals.
.sam file       # Read alignments with event tags produced by f5c

User guide provides example code for generating the SWARM inputs from pod5/fast5 files.