Repositories list

• SampleSheetGenerator

  Public
  but in flask!

  Python

  •0•0•6•0•Updated Dec 10, 2024Dec 10, 2024

• 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

  •423•0•0•0•Updated Jul 4, 2024Jul 4, 2024

• nfcore_smrnaseq

  Public
  A small-RNA sequencing analysis pipeline

  Nextflow

  •

  MIT License

  •127•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

  •717•0•0•1•Updated Jan 15, 2024Jan 15, 2024

• Yggdrasil

  Public
  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

  •147•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

  •41•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