Repositories list

• Broker4Microbiota

  Public
  Django App for collection and storage of sequencing orders for the sequencing facility

  JavaScript

  •

  MIT License

  •0•1•53•0•Updated Oct 20, 2025Oct 20, 2025

• seminar-dlmb-2025-winter-public

  Public
  Materials for the "Seminar: Deep Learning for Molecular Biology" on 2025W at TU Braunschweig (https://www.helmholtz-hzi.de/en/research/research-topics/bacterial-and-viral-pathogens/computational-biology-of-infection-research/workshop/seminar-deep-learning-for-molecular-biology/)

  Jupyter Notebook

  •0•0•0•0•Updated Oct 6, 2025Oct 6, 2025

• Corona_Variant_Scoring

  Public
  Method to score circulating SARS-CoV-2 lineages on their potential antigenicity

  vaccinessars-cov-2antigenicity+ 1immune-escape

  HTML

  •

  Other

  •0•1•0•0•Updated Jul 29, 2025Jul 29, 2025

• mag

  Public
  Best practice pipeline for assembly and binning of metagenomes based on CAMI2 challenge, adapted from nf-core/mag

  Nextflow

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  MIT License

  •141•1•2•0•Updated Jul 10, 2025Jul 10, 2025

• corona_protein_dynamics

  Public
  Mutation dynamics analysis of SARS-Cov-2 S-protein based on phylogenetics and statistics

  Python

  •

  Other

  •0•1•0•0•Updated Apr 30, 2025Apr 30, 2025

• corona_lineage_dynamics

  Public
  SDPlots scripts for the coverage server

  C++

  •

  Other

  •0•2•0•0•Updated Apr 30, 2025Apr 30, 2025

• seminar-dlmb-2025-summer-public

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Apr 10, 2025Apr 10, 2025

• phylogeny-of-single-cells

  Public
  snakemake workflow for the phylogenetic reconstruction of single cell lineages from multiple displacement amplified single cell DNAseq

  Python

  •

  MIT License

  •1•0•0•1•Updated Mar 24, 2025Mar 24, 2025

• ChemLM

  Public
  Jupyter Notebook

  •

  Academic Free License v3.0

  •0•1•0•0•Updated Mar 2, 2025Mar 2, 2025

• phylogeo-tools

  Public
  C++

  •0•1•0•0•Updated Jan 27, 2025Jan 27, 2025

• AMR_benchmarking

  Public
  Python

  •

  MIT License

  •0•5•0•0•Updated Nov 29, 2024Nov 29, 2024

• seminar-dlmb-2024-winter-public

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Oct 14, 2024Oct 14, 2024

• AMR_prediction_pipeline

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Sep 10, 2024Sep 10, 2024

• epitope-prediction

  Public
  Python

  •

  GNU General Public License v3.0

  •11•18•1•2•Updated Jun 10, 2024Jun 10, 2024

• AntigenicTreeTools

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated May 21, 2024May 21, 2024

• fastml

  Public
  A copy of https://github.com/AidanDelaney/fastml with errors fixed

  C++

  •0•0•0•0•Updated May 17, 2024May 17, 2024

• covid-germany-mcmc

  Public
  SARS-CoV-2 lineage importations and spread are reduced after nonpharmaceutical interventions in phylogeographic analyses

  HTML

  •0•2•0•0•Updated Apr 11, 2024Apr 11, 2024

• taxprofiler

  Public
  Highly parallelised multi-taxonomic profiling of shotgun metagenomic data

  Nextflow

  •

  MIT License

  •57•0•0•0•Updated Apr 3, 2024Apr 3, 2024

• RiboDetector

  Public
  Accurate and rapid RiboRNA sequences Detector based on deep learning

  Python

  •

  GNU General Public License v3.0

  •15•115•8•0•Updated Jan 10, 2024Jan 10, 2024

• ngs_form

  Public
  HTML

  •0•0•0•0•Updated Nov 21, 2023Nov 21, 2023

• covid-germany-mcmc-one-tree-public

  Public
  R

  •0•0•0•0•Updated Oct 10, 2023Oct 10, 2023

• covid-germany-mcmc-phylogeo-tools

  Public
  A phylogeo-tools for covid-germany-mcmc

  C++

  •0•0•0•0•Updated Oct 10, 2023Oct 10, 2023

• Haploflow

  Public
  C++

  •

  GNU General Public License v3.0

  •3•30•6•0•Updated Sep 21, 2023Sep 21, 2023

• epitope-prediction-paper

  Public
  Data and results for the EpitopeVec paper

  Python

  •4•8•0•2•Updated Jul 6, 2023Jul 6, 2023

• hcv-mds

  Public
  Neutralization maps for HCV data

  Python

  •0•0•2•2•Updated Jul 6, 2023Jul 6, 2023

• lotus

  Public
  Scripts related to the Lotus japonicus root microbiota manuscript Zgadzaj, Garrido-Oter et al., 2016

  R

  •7•0•0•1•Updated Jul 3, 2023Jul 3, 2023

• scelestial

  Public
  0•0•0•0•Updated Jun 10, 2023Jun 10, 2023

• Quasimodo

  Public
  QuasiModo: Assessing viral genomic analysis methods on HCMV strain mixture

  benchmarkingmetagenomicsviral-genomics

  C++

  •

  GNU General Public License v3.0

  •3•12•1•0•Updated Sep 22, 2022Sep 22, 2022

• scelestial-paper-materials-devel

  Public
  The lineage tree reconstruction method based on Steiner tree problem - dataset and test scripts for the paper (development version)

  C++

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated May 30, 2022May 30, 2022

• Haploflow_supplementary

  Public
  Helper scripts and other supplementary material for Haploflow

  Python

  •0•0•1•0•Updated May 6, 2022May 6, 2022