nf-core
Published June 17, 2026 | Version 2.18.0
Software Open

nf-core/ampliseq: Ampliseq Version 2.18.0

Authors/Creators

  • 1. Quantitative Biology Center (QBiC)
  • 2. National Bioinformatics Infrastructure Sweden (NBIS)
  • 3. Linnaeus University & Stockholm University
  • 4. Boehringer Ingelheim
  • 5. UNESCO
  • 6. PeriMatrix IT Consultancy
  • 7. OceanOmics Centre at the University of Western Australia
  • 8. @NBISweden
  • 9. Lund University
  • 10. QBiC @qbicsoftware
  • 11. HUJI
  • 12. Universidad Andrés Bello
  • 13. Analysis and Bioinformatics for Marine Science (ABiMS)
  • 14. Data Science Centre, EMBL
  • 15. Cirro Bio
  • 16. APHL-CDC Public Health Laboratory Fellow (Bioinformatics)
  • 17. @Syngenta
  • 18. Seqera
  • 19. STFC Hartree Centre
  • 20. @ScilifelabDataCentre

Description

nf-core/ampliseq version 2.18.0 - 2026-06-17

Summary of changes

  • Changed default taxonomy database: The default reference taxonomy changed from SILVA 138.2 to SBDI-GTDB R11-RS232-1
  • New taxonomic assignment method: VSEARCH/LCA taxonomic assignment was added with built-in reference databases (coidb, midori2-co1, unite-fungi, unite-alleuk) and support for custom databases
  • Additional differential abundance analysis: ANCOM-BC2 was added alongside existing ANCOM and ANCOM-BC methods
  • Major dependency upgrades: QIIME2 was upgraded from 2024.10.1 to 2026.04.0
  • Quality control improvements: Added binned quality score detection with a warning system

Detailed changes

Added

  • #992 - Slack notification on status of AWS full test (by @d4straub)
  • #998 - Added taxonomic assignment with VSEARCH/LCA. This adds parameters --vsearch_lca_ref_taxonomy for built-in reference databases (supports coidb, midori2-co1, unite-fungi, unite-alleuk) and --vsearch_lca_ref_tax_custom for custom reference databases, as well as other VSEARCH/LCA related parameters. (by @pieterprovoost)
  • #1001 - Add ANCOM-BC2 alongside ANCOM and ANCOM-BC (by @d4straub)
  • #1009,#1012 - Add SBDI-GTDB and GTDB databases for release R11-RS232 (by @erikrikarddaniel)
  • #1011 - Warn if read quality scores appear binned, but allow override with --ignore_binned_quality (by @d4straub)

Changed

  • #1010 - Profile apptainer uses now singularity container instead of converting docker containers (by @d4straub)
  • #1012 - Changed default for --dada_ref_taxonomy from silva=138.2 to sbdi-gtdb=R11-RS232-1 (by @d4straub)
  • #1013 - Bump pipeline version and add github handles to change documentation (by @d4straub)
  • #1016 - Increase resources for several resource-limited processes (by @d4straub)

Fixed

  • #993 - Rely on topics for software versions (by @d4straub)
  • #999 - Template update for nf-core/tools version 4.0.2 (by @d4straub)
  • #1009 - Reintroduce phylogenetic placement in SBDI-GTDB trees (by @erikrikarddaniel)
  • #1009 - Make sure clustalo is the default alignment program for phylogenetic placement, as the docs say (by @erikrikarddaniel)

Dependencies

  • #998 - Added taxonomic assignment with VSEARCH/LCA. Updates samtools and vsearch. (by @pieterprovoost)
  • #999 - MultiQC 1.33 to 1.34 (by @d4straub)
  • #1000 - QIIME2 2024.10.1 to 2026.04.0 (by @d4straub)
  • #1006 - nf-schema from 2.5.1 to 2.7.2 (by @d4straub)

| software | previously | now | | -------- | ---------- | --------- | | MultiQC | 1.33 | 1.34 | | QIIME2 | 2024.10.1 | 2026.04.0 | | samtools | 1.16.1 | 1.21.1 | | vsearch | 2.21.1 | 2.31.0 |

Removed

  • #992 - Remove hook_url from the pipeline configuration (by @d4straub)

Files

nf-core/ampliseq-2.18.0.zip

Files (2.0 MB)

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md5:7430c294e816f6871a5a0ecffa8c0c81
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Additional details

Related works

Is supplement to
Software: https://github.com/nf-core/ampliseq/tree/2.18.0 (URL)

Software

Repository URL
https://github.com/nf-core/ampliseq