Repositories list

• barcode_validator

  Public
  Standardized validation of barcodes

  Python

  •

  Apache License 2.0

  •5•1•6•0•Updated Aug 7, 2025Aug 7, 2025

• galaxy-tool-edentity-metabarcoding-pipeline

  Public
  Python

  •

  Apache License 2.0

  •0•1•0•1•Updated Aug 7, 2025Aug 7, 2025

• BGE_data_processing_skimming

  Public
  BGE sample download, checksum, sample-range, plate-split; prep for MGE

  Shell

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 5, 2025Aug 5, 2025

• sdmdl

  Public
  Species Distribution Modelling using Deep Learning

  biodiversity-patternsecological-niche-modellingdl-sdm+ 1deep-learning

  Python

  •

  MIT License

  •11•24•4•21•Updated Aug 1, 2025Aug 1, 2025

• galaxy-tool-structural-validator

  Public
  Galaxy tool for structural validation of DNA barcode data

  Apache License 2.0

  •0•0•0•0•Updated Jun 30, 2025Jun 30, 2025

• DWCAConfig

  Public
  DWCA Configuratie bestanden om data te downloaden uit ES (NBA)

  Shell

  •2•1•1•1•Updated Jun 25, 2025Jun 25, 2025

• galaxy-tool-beast2

  Public
  Beast2 respository for the Galaxy tool shed

  2•0•0•0•Updated Jun 6, 2025Jun 6, 2025

• mebioda

  Public
  Course repository for Methods in Biodiversity Analysis

  HTML

  •

  MIT License

  •83•22•7•0•Updated Jun 6, 2025Jun 6, 2025

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.6k•0•0•0•Updated May 14, 2025May 14, 2025

• galaxy-tool-BLAST

  Public
  A new tool and wrapper for the identification with blastn

  Python

  •2•0•2•0•Updated Apr 29, 2025Apr 29, 2025

• barcode-constrained-phylogeny-backbone

  Public
  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Mar 24, 2025Mar 24, 2025

• barcode-phylogenetic-diversity

  Public
  Repository for experiments with QIIME-based alpha/beta PD metrics

  Python

  •

  Apache License 2.0

  •0•0•5•0•Updated Mar 21, 2025Mar 21, 2025

• barcode-constrained-phylogeny

  Public
  Pipeline for building topologically-constrained phylogenies from DNA barcode data

  phylogeneticsphylogenetic-diversitymetabarcoding+ 2phylogenetic-placementdna-barcoding

  Python

  •

  Apache License 2.0

  •3•2•21•1•Updated Mar 13, 2025Mar 13, 2025

• barcode-classify-protax-fungi

  Public
  Profiling PROTAX-fungi for quick and coarse classification of ITS metabarcoding reads

  HTML

  •

  Apache License 2.0

  •0•0•0•0•Updated Mar 9, 2025Mar 9, 2025

• barcode-skimming-analysis

  Public
  Repository that analyses the success rates of genome skimming for the BGE project

  R

  •

  Apache License 2.0

  •0•0•0•0•Updated Feb 25, 2025Feb 25, 2025

• edentity-metabarcoding-phylodiv

  Public
  Shell scripts for prototyping a QIIME2

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Feb 17, 2025Feb 17, 2025

• nba-brondata-bijzcol

  Public
  Bron data set for NBA on bijzondere collecties

  Apache License 2.0

  •0•0•0•0•Updated Feb 15, 2025Feb 15, 2025

• edentity-sequencer-qc

  Public
  scripts for comparing sequencer outputs

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Dec 4, 2024Dec 4, 2024

• BGE-gaplist

  Public
  Pipeline for generating and updating the BGE gap list

  Perl

  •

  Apache License 2.0

  •0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

• evobio2

  Public
  EvBio2 UL computer practicum

  GNU General Public License v3.0

  •0•0•0•0•Updated Sep 6, 2024Sep 6, 2024

• barcode-classify-transformer

  Public
  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Jun 12, 2024Jun 12, 2024

• mycodiversity

  Public
  Pipelines for analyzing fungal diversity

  Python

  •

  MIT License

  •1•1•0•3•Updated May 26, 2024May 26, 2024

• galaxy-tool-lca

  Public
  Python

  •2•3•1•0•Updated Apr 9, 2024Apr 9, 2024

• DNABERT_S

  Public
  DNABERT_S: Learning Species-Aware DNA Embedding with Genome Foundation Models

  Python

  •28•0•0•0•Updated Mar 21, 2024Mar 21, 2024

• galaxy-tool-make-otu-table

  Public
  Python

  •0•0•0•0•Updated Mar 21, 2024Mar 21, 2024

• browbrow

  Public
  Brownian motion in a browser window

  Creative Commons Zero v1.0 Universal

  •0•0•4•0•Updated Feb 28, 2024Feb 28, 2024

• galaxy-pipeline-hybseq

  Public
  End-to-end implementation of HybSeq analysis in Naturalis's Galaxy portal

  Python

  •

  MIT License

  •1•0•1•0•Updated Feb 19, 2024Feb 19, 2024

• galaxy-tool-taxonmatcher

  Public
  Find for your input taxonomy the taxonomy from an other database

  Python

  •0•4•1•0•Updated Jan 31, 2024Jan 31, 2024

• bioblend-test

  Public
  Example implementation of bioblend galaxy client

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 25, 2024Jan 25, 2024

• snakemake-parallel-test

  Public
  Perl

  •

  Apache License 2.0

  •0•0•0•0•Updated Dec 15, 2023Dec 15, 2023