nf-core

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Published October 6, 2025 | Version 2.15.0
Software Open

nf-core/ampliseq: Ampliseq Version 2.15.0

Authors/Creators

  • 1. Quantitative Biology Center (QBiC)
  • 2. National Bioinformatics Infrastructure Sweden (NBIS)
  • 3. Linnaeus University & Stockholm University
  • 4. Boehringer Ingelheim
  • 5. PeriMatrix IT Consultancy
  • 6. OceanOmics Centre at the University of Western Australia
  • 7. @NBISweden
  • 8. Lund University
  • 9. HUJI
  • 10. QBiC @qbicsoftware
  • 11. Analysis and Bioinformatics for Marine Science (ABiMS)
  • 12. Data Science Centre, EMBL
  • 13. @FredHutch
  • 14. APHL-CDC Public Health Laboratory Fellow (Bioinformatics)
  • 15. @Syngenta
  • 16. STFC Hartree Centre
  • 17. Seqera
  • 18. CNRS, Station Biologique
  • 19. CoBiG²
  • 20. @seqeralabs
  • 21. Seqera Labs

Description

nf-core/ampliseq version 2.15.0 - 2025-10-06

Summary of changes

Many issues were fixed and more control was given over QC and taxonomic classification.

Detailed changes

Added

  • #909,#914 - Parameter --truncq allows read truncation by quality score, where each read is truncated at the first instance of a quality score less than or equal to truncq (default value is 2). This quality score-based truncation occurs before read length truncation. If --trunc_qmin and --trunc_rmin are used to automatically calculate the values for trunclenf and trunclenr used for read length truncation, those calculations are based on the read metrics before quality score-based truncation (using truncq) is performed. truncq is passed directly as truncQ into DADA2's filterAndTrim method.
  • #913 - Parameter --dada_min_boot allows the user to specify a minimum bootstrap confidence (out of 100 trials) for assigning a taxonomic level with DADA2's assignTaxonomy method.

Changed

  • #903 - Corrects a broken link for midori2-co1 database.

Fixed

  • #893,#896,#905,#912 - Template update for nf-core/tools version 3.3.2 and reorganization of nf-test
  • #897 - Allow multiple region analysis with one sample.
  • #899 - With --dada_ref_tax_custom all chunks defined by --dada_assign_chunksize are now taxonomically annotated.
  • #904 - Update untar module.
  • #906 - Fix --mergepairs_strategy "consensus" causing an error in dada2_stats when analysing a run composed by only one sample.

Removed

  • #894 - Remove BOLD databases plantae-bold-its1 & plantae-bold-trnL, for plant samples with markers ITS1 and trnL, versions 20240510. Database included low quality sequences.

Files

nf-core/ampliseq-2.15.0.zip

Files (1.8 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/nf-core/ampliseq/tree/2.15.0 (URL)

Software

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