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@nioo-knaw Netherlands Institute of Ecology (NIOO-KNAW)

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    13 repositories

    • epiGBS2

      Public
      This is the epiGBS2 snakemake pipeline as published in a preprint version.
      Python
      •
      MIT License
      •6•2•9•1•Updated May 15, 2024May 15, 2024

    • hydra

      Public archive
      Pipeline for amplicon sequencing projects. OTUs can be build with various methods (usearch,vsearch,uparse,swarm) and classified using the RDP Classifier and SINA. Final output is a BIOM file for downstream processing (Phyloseq/R)
      snakemakemetagenomics16smetagenomic-analysisits18samplicon-sequencing
      Python
      •
      MIT License
      •1•0•0•0•Updated Dec 18, 2023Dec 18, 2023

    • orochi

      Public archive
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Dec 18, 2023Dec 18, 2023

    • PhyloFunDB

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 24, 2022May 24, 2022

    • BSAnalyser

      Public
      BSAnalyser is a pipeline designed to benchmark multiple BS aligners and SNP callers from raw BS sequencing data input. It will align sequences using the chosen aligners and call SNPs using the chosen SNP calling tools for each aligner used.
      Python
      •
      MIT License
      •1•0•0•0•Updated Jul 27, 2020Jul 27, 2020

    • HFC-permutation

      Public
      pipeline for HFC calculations from ped and map file, including permutations
      Shell
      •
      MIT License
      •1•0•0•0•Updated Jul 24, 2020Jul 24, 2020

    • QC-NGS

      Public
      This tutorial will guide you through the process of generating and reading a QC report.
      HTML
      •1•0•0•0•Updated Jun 3, 2019Jun 3, 2019

    • 2019-02-05-wageningen-genomics

      Public
      Python
      •
      Other
      •2•0•0•0•Updated Feb 4, 2019Feb 4, 2019

    • cloud-genomics

      Public
      Python
      •
      Other
      •2•2•0•0•Updated Jan 30, 2019Jan 30, 2019

    • wrangling-genomics

      Public
      HTML
      •
      Other
      •0•0•0•0•Updated Jan 29, 2019Jan 29, 2019

    • epiGBS

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Dec 13, 2018Dec 13, 2018

    • epiGBS-pipeline

      Public
      modified clone from https://github.com/thomasvangurp/epiGBS. Added wrapper scripts and conda compatibility
      Python
      •0•0•0•0•Updated Dec 4, 2018Dec 4, 2018

    • PhyloProfiler

      Public
      0•0•0•0•Updated May 30, 2017May 30, 2017