Release Ampliseq Version 2.18.0 · nf-core/ampliseq

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

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

#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)

#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)

#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)

#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)