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    • mag

      Public
      Best practice pipeline for assembly and binning of metagenomes based on CAMI2 challenge, adapted from nf-core/mag
      Nextflow
      MIT License
      111120Updated Dec 11, 2024Dec 11, 2024
    • Django App for collection and storage of sequencing orders for the sequencing facility
      JavaScript
      0020Updated Dec 10, 2024Dec 10, 2024
    • Method to score circulating SARS-CoV-2 lineages on their potential antigenicity
      HTML
      Other
      0000Updated Dec 5, 2024Dec 5, 2024
    • snakemake workflow for the phylogenetic reconstruction of single cell lineages from multiple displacement amplified single cell DNAseq
      Python
      MIT License
      1001Updated Dec 2, 2024Dec 2, 2024
    • Python
      MIT License
      0300Updated Nov 29, 2024Nov 29, 2024
    • SDPlots scripts for the coverage server
      C++
      Other
      0120Updated Nov 24, 2024Nov 24, 2024
    • ChemLM

      Public
      Python
      Academic Free License v3.0
      0100Updated Oct 21, 2024Oct 21, 2024
    • Jupyter Notebook
      0100Updated Oct 14, 2024Oct 14, 2024
    • Python
      MIT License
      0000Updated Sep 10, 2024Sep 10, 2024
    • Python
      GNU General Public License v3.0
      111502Updated Jun 10, 2024Jun 10, 2024
    • Java
      GNU General Public License v3.0
      0000Updated May 21, 2024May 21, 2024
    • fastml

      Public
      A copy of https://github.com/AidanDelaney/fastml with errors fixed
      C++
      0000Updated May 17, 2024May 17, 2024
    • SARS-CoV-2 lineage importations and spread are reduced after nonpharmaceutical interventions in phylogeographic analyses
      HTML
      0200Updated Apr 11, 2024Apr 11, 2024
    • Highly parallelised multi-taxonomic profiling of shotgun metagenomic data
      Nextflow
      MIT License
      36000Updated Apr 3, 2024Apr 3, 2024
    • Mutation dynamics analysis of SARS-Cov-2 S-protein based on phylogenetics and statistics
      Python
      Other
      0000Updated Mar 28, 2024Mar 28, 2024
    • Accurate and rapid RiboRNA sequences Detector based on deep learning
      Python
      GNU General Public License v3.0
      169970Updated Jan 10, 2024Jan 10, 2024
    • ngs_form

      Public
      HTML
      0000Updated Nov 21, 2023Nov 21, 2023
    • R
      0000Updated Oct 10, 2023Oct 10, 2023
    • A phylogeo-tools for covid-germany-mcmc
      C++
      0000Updated Oct 10, 2023Oct 10, 2023
    • Haploflow

      Public
      C++
      GNU General Public License v3.0
      32960Updated Sep 21, 2023Sep 21, 2023
    • Data and results for the EpitopeVec paper
      Python
      3502Updated Jul 6, 2023Jul 6, 2023
    • hcv-mds

      Public
      Neutralization maps for HCV data
      Python
      0022Updated Jul 6, 2023Jul 6, 2023
    • lotus

      Public
      Scripts related to the Lotus japonicus root microbiota manuscript Zgadzaj, Garrido-Oter et al., 2016
      R
      7001Updated Jul 3, 2023Jul 3, 2023
    • 0000Updated Jun 10, 2023Jun 10, 2023
    • Quasimodo

      Public
      QuasiModo: Assessing viral genomic analysis methods on HCMV strain mixture
      C++
      GNU General Public License v3.0
      31310Updated Sep 22, 2022Sep 22, 2022
    • 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
      0200Updated May 30, 2022May 30, 2022
    • Helper scripts and other supplementary material for Haploflow
      Python
      0010Updated May 6, 2022May 6, 2022
    • A small Snakemake workflow to remove contaminating vector sequences from raw sequencing data using UniVec.
      Python
      MIT License
      0000Updated Feb 3, 2022Feb 3, 2022
    • sankoff

      Public
      C++
      0000Updated Dec 31, 2021Dec 31, 2021
    • Testing of phylogenetic inference methods
      R
      GNU General Public License v2.0
      3000Updated Oct 19, 2021Oct 19, 2021