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    14 repositories

    • SampleSheetGenerator

      Public archive
      but in flask!
      Python
      •0•0•6•1•Updated Sep 19, 2025Sep 19, 2025

    • singleCellWorkflows

      Public
      Nextflow
      •
      MIT License
      •1•0•3•0•Updated Jul 17, 2024Jul 17, 2024

    • nfcore_sarek

      Public
      Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
      Nextflow
      •
      MIT License
      •499•0•0•0•Updated Jul 4, 2024Jul 4, 2024

    • nfcore_smrnaseq

      Public
      A small-RNA sequencing analysis pipeline
      Nextflow
      •
      MIT License
      •131•0•0•0•Updated May 2, 2024May 2, 2024

    • Templates

      Public
      0•0•2•0•Updated Mar 12, 2024Mar 12, 2024

    • nfcore_rnaseq

      Public
      RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
      Nextflow
      •
      MIT License
      •829•0•0•1•Updated Jan 15, 2024Jan 15, 2024

    • Yggdrasil

      Public archive
      the backbone of the CTG pipelines
      Nextflow
      •0•0•0•1•Updated Nov 22, 2023Nov 22, 2023

    • nfcore_methylseq

      Public
      Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
      Nextflow
      •
      MIT License
      •162•0•0•0•Updated Nov 10, 2023Nov 10, 2023

    • wiki

      Public
      0•0•0•0•Updated Sep 1, 2023Sep 1, 2023

    • references

      Public
      bed files
      MIT License
      •0•0•0•0•Updated Aug 10, 2023Aug 10, 2023

    • ctg-lund.github.io

      Public
      QA for CTG
      0•0•0•0•Updated Jun 16, 2023Jun 16, 2023

    • demultiplex

      Public
      Demultiplexing pipeline for sequencing data (nf-core + ctg)
      Nextflow
      •
      MIT License
      •46•0•0•0•Updated Feb 1, 2023Feb 1, 2023

    • pretty_csv

      Public archive
      works on lsens!
      Python
      •1•0•0•0•Updated Nov 18, 2022Nov 18, 2022

    • ctg-sc-rna-10x

      Public
      nextflow pipeline for 10x sc rna analysis
      Shell
      •0•1•0•0•Updated Mar 28, 2022Mar 28, 2022