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 reference k-mers. 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.

Full Documentation : https://hasindu2008.github.io/f5c/docs/overview
Latest release : https://github.com/hasindu2008/f5c/releases/latest
Pre-print : https://doi.org/10.1101/756122
Publication : https://doi.org/10.1186/s12859-020-03697-x

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