Repositories list

• rereference

  Public
  A tool for repositioning reads in a bam file relative to a different reference sequence. This is great if you want to align a SARS-CoV-2 sample to one of the more recent lineages and then reposition the coordinated to match the positions where the reads would map to the original Wuhan-Hu-1 reference sequence.

  Python

  •0•0•0•0•Updated Jan 15, 2025Jan 15, 2025

• platform-compare

  Public
  Comparison of sequencing platforms with a control dataset

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Oct 25, 2024Oct 25, 2024

• freyja-plot

  Public
  Plotting lineage abundance for individual samples from aggregated freyja demix results

  HTML

  •

  MIT License

  •0•0•0•0•Updated Jul 31, 2024Jul 31, 2024

• benchmark-deconvolute

  Public
  Benchmark Dataset Evaluation & COmparison of Nifty, Versatile, Objective Lineage-Unscrambling-Tool Execution

  HTML

  •

  MIT License

  •1•2•0•0•Updated May 28, 2024May 28, 2024

• covid-analysis

  Public
  SARS-CoV-2 sequencing and strain identification pipeline for nanopore samples

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Mar 13, 2024Mar 13, 2024

• ncbi-submit

  Public
  A tool to prepare files and run/monitor programmatic submissions to NCBI

  ftpuploadncbi-genbank+ 4ncbisubmissionncbi-srancbi-biosamples

  Python

  •

  MIT License

  •0•3•0•0•Updated Mar 5, 2024Mar 5, 2024

• dropout

  Public
  Checks for new ampilcon dropouts

  0•0•0•0•Updated Sep 20, 2023Sep 20, 2023

• gisaid-download

  Public
  Assisted download of selected samples from GISAID

  metadatasequencinggisaid+ 1gisaid-download

  Python

  •

  MIT License

  •0•1•1•0•Updated Mar 17, 2023Mar 17, 2023

• hpc-interact

  Public
  Useful for scripting file transfer (sftp) and sending commands (ssh) to hpc - a wrapper for `expect`

  Python

  •

  MIT License

  •0•0•0•0•Updated Mar 17, 2023Mar 17, 2023