Popular repositories

1. ncbi-submit ncbi-submit Public

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

   Python 2

2. benchmark-deconvolute benchmark-deconvolute Public

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

   HTML 2

3. hpc-interact hpc-interact Public

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

   Python

4. gisaid-download gisaid-download Public

   Assisted download of selected samples from GISAID

   Python

5. covid-analysis covid-analysis Public

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

   Nextflow

6. freyja-plot freyja-plot Public

   Plotting lineage abundance for individual samples from aggregated freyja demix results

   HTML