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Published September 27, 2020 | Version v1.5.0
Software Open

nextgenusfs/amptk: amptk v1.5.0

Authors/Creators

  • 1. @RedVentures
  • 2. University of California-Riverside
  • 3. IPAE

Description

  • 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.

Files

nextgenusfs/amptk-v1.5.0.zip

Files (2.4 MB)

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md5:177af72a76360e646703eea00e0553ff
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Additional details

Related works

Is supplement to
https://github.com/nextgenusfs/amptk/tree/v1.5.0 (URL)