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Omar Ahmed edited this page Jul 25, 2024
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- 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.
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- Using minimizer alphabet to represent reference and reads
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- Using a look-up table called ftab to speed-up query
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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.
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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.
- When using the
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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.
- 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
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The intuition here is that since Cliffy is doing backward search, we can use a lookup table to skip some initial steps.
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How do I use it?
- When using the
build
sub-command: theftab
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.
- When using the