nf-core

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Published March 2, 2023 | Version 2.5.0
Software Open

nf-core/ampliseq: Ampliseq Version 2.5.0

Authors/Creators

  • 1. QBiC
  • 2. National Bioinformatics Infrastructure Sweden (NBIS)
  • 3. Boehringer Ingelheim
  • 4. Linnaeus University & Stockholm University
  • 5. @NBISweden
  • 6. HUJI
  • 7. @qbicsoftware
  • 8. Seqera Labs
  • 9. @seqeralabs | Stockholm
  • 10. @seqeralabs
  • 11. AIRAmed

Description

nf-core/ampliseq version 2.5.0 - 2023-03-02 Summary of changes
  • Added COIDB DADA2 taxonomic database
  • Small adjustments to taxonomic classification, ASV filtering by barrnap, fasta input
  • sbdi-export works for more taxonomic databases now
  • nf-core template update from 2.6 to 2.7.2
Detailed changes Added
  • #518,#534 - Add COIDB DADA2 reference taxonomy database
  • #521 - Export svg in addition to pdf files for quality plots from DADA2
  • #538 - Parameter --diversity_rarefaction_depth controls the minimum rarefaction depth for diversity analysis, this allows increasing the rarefaction depth at the cost of excluding low count samples. Parameter --ancom_sample_min_count sets the minimum sample counts to retain a sample for ANCOM analysis.
Changed
  • #537 - Update output generated with option sbdi-export
  • #541 - Remove adjustments of taxonomic levels for RDP & SILVA & GTDB & UNITE database for DADA2 taxonomic classification, reduced default of --dada_tax_agglom_max from 7 to 6
  • #548 - --filter_ssu accepted any barrnap hit to a kingdom (domain) (any occurence in resulting gff) to choose an ASV, now only ASVs with the kingdom (domain) that has the lowest evalue are accepted.
Fixed
  • #513 - Template update for nf-core/tools version 2.7.2
  • #519 - Adding the pipeline reference to the MultiQC report
  • #520,#530 - Fix conda packages
  • #531,#546 - Update documentation
  • #535 - Make sure barrnap runs with fasta input
  • #544 - Adding module to fix header in fasta input if needed
Dependencies
  • #528 - Updated QIIME2
Tool Previous version New version
QIIME2 2022.8 2022.11
Removed
  • #513 - Removed parameter --enable_conda.

Files

nf-core/ampliseq-2.5.0.zip

Files (3.5 MB)

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Additional details

Related works

Is supplement to
https://github.com/nf-core/ampliseq/tree/2.5.0 (URL)