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scrappie website  

Scrappie is a technology demonstrator for the Oxford Nanopore Technologies Limited Research Algorithms group.

Basic usage:

  • scrappie events Base call from event based data.
  • scrappie help Print general help or help about specific Scrappie command.
  • scrappie licence Print licensing information.
  • scrappie raw Base call directly from raw signal.
  • scrappie version Print version information.
  • scrappie squiggle Create approximate squiggle for sequence
  • scrappie mappy Map signal to approximate squiggle
  • scrappie seqmappy Map signal to sequence via basecall posteriors
  • scrappie event_table Output table of events for read

This project began life as a proof (bet) that a base caller could be written in a low level language in under 8 hours. Some of the poor and just plain odd design decisions, along with the lack of documentation, are a result of its inception. In keeping with ONT's fish naming policy, the project was originally called Crappie.

Scrappie's purpose is to demonstrate the next generation of base calling and, as such, may change drastically between releases and breaks backwards compatibility. Newer versions may drop support of current features or change their behaviour.

Environment Modules

Run module spider scrappie to find out what environment modules are available for this application.

System Variables

  • HPC_SCRAPPIE_DIR - installation directory
  • HPC_SCRAPPIE_BIN - executabledirectory