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v2.0.0

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@seina001 seina001 released this 30 Jun 20:22
· 106 commits to main since this release
v2.0.0
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Release Highlights

  • Removed BBmap dependency
    • BBmap scripts are no longer used in the pipeline, including:
      • reformat.sh (interleaved files no longer supported)
      • bbmerge.sh (merging of paired-end reads now done with Vsearch --fastq_mergepairs)
        • merging of paired-end reads is different between Vsearch and BBmerge, so results may differ
  • Updated dereplication step for newer versions of Vsearch
    • Dereplication step now done using Vsearch --fastx_uniques (derep_fulllength command no longer supports fastq files)
  • Qiime2 plugin version of ITSxpress is now part of the standalone package of ITSxpress
    • No longer need to install q2-itsxpress separately and will be installed if Qiime2 is already installed, otherwise only the standalone version will be installed
    • Qiime2 plugin version of ITSxpress is no longer maintained after q2-itsxpress v1.8.1
  • Pacbio sequences are now supported if fastq file scores are in Illumina format
    Bug Fixes
  • Fixed bug where the itsxpress qiime plugin was not handling single-end reads correctly, and was looking for a reverse read file
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