Recommended Settings

• There are two main speed optimizations that are important to keep in mind when using Cliffy to make sure you are taking advantage of them.
  • 1. Using minimizer alphabet to represent reference and reads
  • 2. Using a look-up table called ftab to speed-up query

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Using minimizer alphabet:

• The basic idea here is that if we digest the database sequence into a concatenated sequence of minimizers where each minimizer is a single 8-bit character. It will reduce the size of the index but it will also reduce the size of reads at query time to speed up query.

• How do I use it?

  • When using the build sub-command to build indexes: use --minimizers option to digest sequence.
  • When running the run sub-command to run queries: use --minimizers option to digest the reads.

• How can I change the parameters of minimizer scheme?

  • Keep in mind, the default parameters are chosen in order to balance speed-up with classification accuracy. However, if you would like to change the parameters. You can do so using the --small-window and --large-window options.

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Using ftab:

• The intuition here is that since Cliffy is doing backward search, we can use a lookup table to skip some initial steps.

• How do I use it?

  • When using the build sub-command: the ftab data-structure will be written to a file by default, so you don't need to do anyting!
  • When using the run sub-command: use the --ftab option in order to use the data-structure to speed-up queries.