f5c is an optimised re-implementation of the call-methylation and eventalign modules in Nanopolish. Given a set of basecalled Nanopore reads and the raw signals, f5c call-methylation detects the methylated cytosine and f5c eventalign aligns raw nanopore DNA signals (events) to the base-called read. f5c can optionally utilise NVIDIA graphics cards for acceleration.
First the reads have to be indexed using
f5c index. Then invoke
f5c call-methylation to detect methylated cytosine bases. Finally, you may use
f5c meth-freq to obtain methylation frequencies. Alternatively, invoke
f5c eventalign to perform event alignment. The results are almost the same as from nanopolish except a few differences due to floating point approximations.