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1. snpkit snpkit Public

   Modular workflow for Microbial Variant Calling and SNP diagnostics.

   Python 5 4

2. samosa samosa Public

   (S)train (A)ssignment from (M)etagen(O)me (S)NP (A)nalysis.

   Jupyter Notebook 3 1

3. Growth-rate-estimate_SMAKE Growth-rate-estimate_SMAKE Public

   Growth-rate-analysis is a Snakemake workflow to calculate peak to through ratio (PTR - ratio of copy numbers at origin of replication to terminus) from mapped reads coverage.

   Jupyter Notebook

4. Nanosake Nanosake Public

   A Snakemake workflow to basecall, quality control and assemble Nanopore data.

   Python 2

5. QCD_SMAKE QCD_SMAKE Public

   Runs Quality Control workflow on Illumina WGS data

   Python