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nextgenusfs/amptk: amptk v1.5.0

Jon Love; Jon Palmer; Jason Stajich; Andreas Sjödin; Vladimir Mikryukov; Franzwagner Ternus

  • to support OSX Catalina dropping 32-bit applications, I've removed usearch9 as a strict dependency. vsearch will be the default for all processing steps, including taxonomy assignment. Along these lines, I've dropped UTAX classifier as "default" in the hybrid taxonomy method.
  • dropping usearch, required addition of a few new dependencies: mafft, fasttree, and the python package pyfastx (for speed simplicity).
  • added support for PacBio CCS reads. Reads can be processed with amptk pacbio and then clustering with amptk pb-dada2
  • several bug fixes
  • working on ONT (Oxford Nanopore) support as well -- stay tuned for this in near future.

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