Skip To Main Content
Sofoklis Keisaris on Muck Rack

Sofoklis Keisaris

Is this you? As a journalist, you can create a free Muck Rack account to customize your profile, list your contact preferences, and upload a portfolio of your best work. Claim your profile
Back to Sofoklis Keisaris’s profile

Articles by Sofoklis Keisaris

nf-core/ampliseq: Ampliseq Version 3.1.0

|
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 -...
Open in Who Shared Issue with article?

nf-core/ampliseq: Ampliseq Version 2.18.0

|
By Boehringer Ingelheim, Diego Brambilla, Sofoklis Keisaris
| zenodo.org
Published June 17, 2026 | Version 2.18.0 Software Open 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...
Open in Who Shared Issue with article?

nf-core/ampliseq: Ampliseq Version 2.17.0

|
By Boehringer Ingelheim, Sofoklis Keisaris, Diego Brambilla
| zenodo.org
Published April 15, 2026 | Version 2.17.0 Software Open nf-core/ampliseq version 2.17.0 - 2026-04-15 sample sheet standardization (legacy sample sheet still allowed) added Decontam for decontamination added ITSxRust alongside ITSx improved phylogenetic placement data handling optimization for binned quality sequencing data local storage for reference databases a bunch of bug fixes #948,#976 - Decontam as optional decontamination tool.
Open in Who Shared Issue with article?
Show More