Repositories list

• Figaro

  Public
  Pipeline for analyzing HIVDR samples sequenced using Oxford Nanopore Technologies (ONT).

  HTML

  •1•1•0•0•Updated Dec 18, 2024Dec 18, 2024

• submission-impossible

  Public
  semi-automated SRA submission scripts

  Jupyter Notebook

  •1•1•0•0•Updated Oct 31, 2024Oct 31, 2024

• coverage_calculator

  Public
  coverage calculator for whole genome assembly

  Python

  •0•0•0•0•Updated May 15, 2024May 15, 2024

• mNGS_SC2

  Public
  metagenomic analysis of sarscov2 patients

  R

  •0•0•0•0•Updated Feb 20, 2024Feb 20, 2024

• Karumata

  Public
  Python

  •0•0•0•0•Updated Oct 25, 2023Oct 25, 2023

• TBtree

  Public
  Nextflow

  •0•0•0•0•Updated Oct 10, 2023Oct 10, 2023

• primer-scheme-v5.3.2

  Public
  Python

  •

  Creative Commons Attribution 4.0 International

  •0•0•0•0•Updated Oct 9, 2023Oct 9, 2023

• kariton

  Public
  Masking of flagged regions and lineage assignment

  Python

  •1•1•1•0•Updated Sep 7, 2023Sep 7, 2023

• subsam_phylo

  Public
  Snakemake workflow for subsampling sequences for phylogenetic/phylodynamic anlaysis.

  Python

  •0•0•0•0•Updated Aug 17, 2023Aug 17, 2023

• mbl-artic

  Public
  Nextflow

  •0•0•0•0•Updated Jul 31, 2023Jul 31, 2023

• primer-schemes

  Public
  Primer schemes for real-time genome epidemiology

  Python

  •

  Creative Commons Attribution 4.0 International

  •42•0•0•0•Updated Jul 14, 2023Jul 14, 2023