Published July 15, 2019 | Version 1.0.0
Software Open

will-rowe/hulk: v1.0.0

  • 1. @stfc
  • 2. @dib-lab - @ucdavis

Description

This is a complete re-implementation of HULK. The change log states the main changes:

  • fully re-written codebase
    • I've aimed for it to be largely backwards compatible with previous releases
  • fully open-sourced!
  • algorithm changes
    • underlying histogram is now based on minimizer frequencies
    • count-min sketch for k-mer frequencies is now replaced with a fixed-size array and a jump-hash for minimizer placement
  • changes to the sketch subcommand:
    • sketches saved to JSON by default (ala sourmash)
    • histosketch count-min sketch is no longer configurable by the user (this was Epsilon and Delta)
    • spectrum size is determined based on k-mer size
    • minCount for k-mer frequencies is removed
  • changes to the smash subcommand:
    • operates on JSON input
    • outputs matrix as csv
  • replaced some unecessary features
    • the functionality of the print and distance subcommands is available in the smash subcommand

Files

will-rowe/hulk-1.0.0.zip

Files (4.0 MB)

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md5:65d9675df19d7837608096cf5e6c99ba
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Additional details

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