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Ampliseq Version 2.8.0
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@d4straub d4straub released this 16 Jan 14:55
· 260 commits to master since this release
2.8.0
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nf-core/ampliseq version 2.8.0 - 2024-01-16

Summary of changes

  • Three additional reference databases available: --qiime_ref_taxonomy greengenes2 (prokaryotic 16S), --dada_ref_taxonomy phytoref (eukaryotic plastid 16S rRNA), --dada_ref_taxonomy zehr-nifh (Nitrogenase iron protein NifH)
  • New parameters --qiime_ref_tax_custom, --skip_qiime_downstream, --dada_taxonomy_rc, and --dada_addspecies_allowmultiple
  • Bug fixes for using phyloseq, VSEARCH, and error messages
  • Updated documentation & reporting
  • Pipeline template update

Detailed changes

Added

  • #666 - Added Greengenes2 database, version 2022.10, support for QIIME2 taxonomic classification.
  • #667,#691 - Added --qiime_ref_tax_custom to permit custom reference database for QIIME2 taxonomic classification
  • #674 - Add PhytoRef database for DADA2 taxonomy assignment using --dada_ref_taxonomy phytoref
  • #675 - Add the Zehr lab nifH database for DADA2 taxonomy assignment using --dada_ref_taxonomy zehr-nifh
  • #681 - For DADA2, with --dada_addspecies_allowmultiple multiple exact species matches are reported and with --dada_taxonomy_rc reverse-complement matches are also considered in taxonomic classification

Changed

  • #677 - Added cut_its information to SDBI export

Fixed

  • #672,#688,#691 - Updated documentation
  • #676 - Phyloseq sometimes only produced one of multiple output files
  • #679 - Prevent masking low complexity regions by VSEARCH with lower case letters
  • #680,#673 - Improved pipeline summary report & error messages
  • #683 - Template update for nf-core/tools version 2.11
  • #687 - Correct conda package for ASV SSU filtering
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