Parameter Profiles


For achieving maximal runtime performance in f5c (call-methylation and eventalign), performance governing parameters must be selected by the user as explained in f5c-perf-hints. From f5c-v0.5 onwards, preset parameter profiles are provided for a wide range of computer systems from embedded systems to servers. The user can simply specify the parameter profile to f5c with -x option followed by the name of the profile (See tables below) that closely matches the specification of the user’s computer system. Performance governing parameters currently set by a profile are t, K, B, max-lf, avg-epk and max-epk. Note that the user can also provide any of these parameters explicitly in addition to a profile. In such a circumstance, parameters set by -x will be overridden by the user provided parameters.

In the tables below, the number of cores includes hyper-threads in Intel processors. The GPU specification can be ignored if you are using the CPU only version of f5c.

Generic profiles

Profile name Description
laptop-low A low-end laptop with a 4-core CPU, 4 GB RAM and a GPU with 2 GB memory
laptop-mid (or simply laptop) A mid-range laptop with an 8-core CPU, 8 GB RAM and a GPU with 3 GB memory
laptop-high A high-end laptop with a 12-core CPU, 16 GB RAM and a GPU with 4 GB memory
desktop-low A low-end workstation with an 8-core CPU, 32 GB RAM and a GPU with 8 GB memory
desktop-mid (or simply desktop) A mid-range workstation with a 12-core CPU, 32 GB RAM and a GPU with 10 GB memory
desktop-high A high-end workstation with a 16-core CPU, 64 GB RAM and a GPU with 12 GB memory
hpc-low A low-end server with a 32-core CPU, 128 GB RAM and a GPU with 16 GB memory
hpc-mid (or simply hpc) A mid-range server with a 48-core CPU, 256 GB RAM and a GPU with 32 GB memory
hpc-high A high-end server with a 64-core CPU, 384 GB RAM and a GPU with 40 GB memory

Specific profiles

Profile name Description
jetson-nano An NVIDIA Jetson Nano with a 4-core CPU and 4 GB integrated memory
jetson-tx2 An NVIDIA Jetson TX2 with a 6-core CPU and 8 GB integrated memory
jetson-xavier An NVIDIA Jetson Xavier with an 8-core CPU and 16 GB integrated memory
nci-gadi A GPU node in the NCI Gadi supercomputer equipped with Tesla V100


  • The above profiles are for a typical nanopore dataset and if your dataset properties (e.g., read lengths, events per k-mer) are quite different, the user may still have to follow steps in f5c-perf-hints for best performance.
  • The above list of computer systems is not exhaustive. I will keep adding new profiles whenever I get hold of a new computer system. If you wish a new profile to be added for a particular computer system, please open an issue.
  • Some of the above profiles are based on values obtained by running f5c-tools. As this method requires a number of iterations and thus very time consuming, some profiles contain interpolated values.
  • The parameter values set by a particular profile can be found here.


This parameters profile feature in f5c was developed by David Hyland.