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Articles by Tom Brekke

nf-core/ampliseq: Ampliseq Version 3.1.0

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By Daniel G. Straub, Daniel Lundin, Alexander Peltzer, Adam Bennett, Tom Brekke, John Sundh, Diego Brambilla, Sofoklis Keisaris, Lokeshwaran Manoharan, Asaf Peer, Aaron O'Brien, Maxime Garcia, Nicolas Henry, Thomas Weber, Matthias Hörtenhuber, Sam Minot, Thom Griffioen, Dan Clayton, Gisela Gabernet, Venkat Malladi, Jeanette Tångrot, Pieter Provoost, Till Englert, Zack Mudge
| zenodo.org
Published October 28, 2026 | Version 3.1.0 nf-core/ampliseq version 3.1.0 - 2026-10-28 SINTAX now accepts the same taxonomic reference databases as DADA2 Consolidation of taxonomic classification can be now done across DADA2, SINTAX and VSEARCH-LCA Fixed MIDORI-CO1 taxonomic reference for SINTAX & VSEARCH_LCA and removed it for DADA2 DADA2 addSpecies with SILVA 144 and Savont now need fewer computational resources The pipeline now also works with Nextflow 26.10 (before 26.04 only) #1123 -...
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nf-core/ampliseq: Ampliseq Version 3.0.0

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By Boehringer Ingelheim, Diego Brambilla, Tom Brekke
| zenodo.org
Published October 9, 2026 | Version 3.0.0 nf-core/ampliseq version 3.0.0 - 2026-10-09 This is a major version update, several parameters and settings of previous versions are not compatible any more, so make sure to read this information and the current pipeline documentation carefully! Most interesting additions: Nanopore/ONT analysis support (R10.4 sequencing preferably with SUP basecalling) with Savont ASV calling Multi-database taxonomy classification with DADA2 with consolidation options...
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