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    48 repositories

    • gbs_prism

      Public
      refactored GBS processing
      Python
      •0•0•1•0•Updated Jan 31, 2025Jan 31, 2025

    • redun.nix

      Public
      A flake package for redun
      Nix
      •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

    • bbmap.nix

      Public
      Nix flake for BBMap, a short-read aligner for DNA and RNA-seq data
      Nix
      •
      MIT License
      •0•0•0•0•Updated Jan 26, 2025Jan 26, 2025

    • KGD

      Public
      Kinship (genetic relatedness) using GBS (genotyping-by-sequencing) with Depth adjustment
      R
      •
      GNU General Public License v2.0
      •16•21•6•0•Updated Jan 19, 2025Jan 19, 2025

    • GBSX

      Public
      GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments
      Java
      •
      GNU General Public License v3.0
      •6•0•0•0•Updated Jan 15, 2025Jan 15, 2025

    • tassel3

      Public
      Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
      Java
      •
      GNU Lesser General Public License v2.1
      •0•0•0•0•Updated Jan 15, 2025Jan 15, 2025

    • bcl-convert.nix

      Public
      Nix Flake for Illumina BCL Convert
      Nix
      •
      MIT License
      •0•0•0•0•Updated Dec 2, 2024Dec 2, 2024

    • cutadapt.nix

      Public
      Flake for cutadapt which removes adapter sequences from sequencing reads
      Nix
      •
      MIT License
      •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

    • wgs_prism

      Public
      Production and q/c for wgs sequencing runs
      Python
      •1•0•0•0•Updated Oct 24, 2024Oct 24, 2024

    • snakemake-playpen

      Public
      Learning SnakeMake
      Nix
      •0•0•0•1•Updated Oct 8, 2024Oct 8, 2024

    • GBS-TaFFE

      Public
      Analysing RE-RRSeq with GTDB taxonomic framework
      Python
      •
      MIT License
      •1•1•0•0•Updated Sep 29, 2024Sep 29, 2024

    • kseq_split

      Public
      kseq_split suite from Tardis extracted as standalone
      C
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Jun 12, 2024Jun 12, 2024

    • GBS_Gender_Predict

      Public
      Using genotyping-by-sequencing to predict gender in animals
      HTML
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Apr 11, 2024Apr 11, 2024

    • seq_prisms

      Public
      Quality control analyses and plots for pools of sequence files
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Oct 16, 2023Oct 16, 2023

    • tardis

      Public
      tardis
      Python
      •
      GNU General Public License v2.0
      •0•1•23•0•Updated Sep 13, 2023Sep 13, 2023

    • melseq_prism

      Public
      melseq prism
      Shell
      •
      GNU General Public License v3.0
      •1•0•4•0•Updated Aug 22, 2023Aug 22, 2023

    • batch_qiime_prism

      Public
      runs batch qiime-based clustering and annotation
      Shell
      •
      GNU General Public License v3.0
      •0•1•2•0•Updated Aug 21, 2023Aug 21, 2023

    • snakemake_example

      Public
      forked_1
      Python
      •1•0•0•0•Updated Jul 6, 2023Jul 6, 2023

    • data_prism

      Public
      R
      •
      GNU General Public License v3.0
      •0•1•1•0•Updated Sep 13, 2022Sep 13, 2022

    • snpGBS

      Public
      A simple bioinformatics workflow to identify single nucleotide polymorphism (SNP) from Genotyping-by-Sequencing (GBS) data.
      snpgbs
      Jupyter Notebook
      •
      MIT License
      •3•1•0•0•Updated Oct 29, 2021Oct 29, 2021

    • brdf

      Public
      Python
      •0•0•0•0•Updated Oct 16, 2020Oct 16, 2020

    • shinyproxy-config-examples

      Public
      Configuration examples for ShinyProxy
      HTML
      •110•0•0•0•Updated Sep 25, 2020Sep 25, 2020

    • Base-Docker-Images

      Public
      Based Docker images used to build other applications.
      Dockerfile
      •0•0•0•0•Updated Sep 24, 2020Sep 24, 2020

    • DataPipelinesAndPrisms

      Public
      Data Pipelines and Prisms Talk at eResearch 2020
      0•0•0•0•Updated Jun 30, 2020Jun 30, 2020

    • resequencing_prism

      Public
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 21, 2020Jun 21, 2020

    • B3-Network

      Public
      0•0•0•1•Updated Jan 16, 2020Jan 16, 2020

    • conda-build-recipes

      Public
      Recipes for building and packaging software packages by using Conda
      Shell
      •0•0•0•0•Updated Dec 19, 2019Dec 19, 2019

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •3.3k•0•0•0•Updated Dec 17, 2019Dec 17, 2019

    • Benchmarks

      Public
      This repository includes benchmarks that will be used to ensure the fit for purpose and to measure the performance of the Scientific Compute Platform in AgResearch.
      R
      •0•1•0•0•Updated Oct 15, 2019Oct 15, 2019

    • run_dbcan

      Public
      Run_dbcan V2, using genomes/metagenomes/proteomes of any orgaisms(prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
      Python
      •
      GNU General Public License v3.0
      •40•0•0•0•Updated Sep 12, 2019Sep 12, 2019