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@Snitkin-Lab-Umich

Snitkin-Lab-Umich

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  1. prewas Public

    R package to perform data pre-processing for more informative bacterial GWAS

    R 5 3

  2. hogwash Public

    Forked from katiesaund/hogwash

    Three bacterial GWAS methods all rolled into one easy-to-use R package

    R 1 1

  3. cognac Public

    Forked from rdcrawford/cognac

    cognac: COre GeNe Alignment Concatenation

    C++ 1

  4. snitkitr Public

    common R functions used in the lab

    R 1 1

  5. regentrans Public

    regentrans: R package for investigating regional pathogen transmission using genomic data

    R 5 1

  6. Comparative_Genomics Public

    Forked from alipirani88/Comparative_Genomics

    Microbial Bioinformatics Workshop

    Shell 1 1

Repositories

Showing 10 of 46 repositories
  • cauris_panaroo Public

    Simple scripts for converting the output of QCD pipelines to be compatible with Panaroo and Orthofinder

    Python 0 0 0 0 Updated Jul 10, 2025
  • pubQCD Public

    Quality control pipeline for datasets downloaded from public databases

    Python 1 0 0 0 Updated Jul 9, 2025
  • strain_validation Public

    Snakemake pipeline to validate mutants made in the lab

    Python 0 0 0 0 Updated Jul 7, 2025
  • QCD Public

    Runs Quality Control workflow on Illumina WGS data

    Python 3 2 2 0 Updated Jun 30, 2025
  • phylokit Public

    Snakemake pipeline to generate a phylogenetic tree from an alignment

    Python 0 0 1 0 Updated Jun 28, 2025
  • cauris_persvade_sv Public

    A snakemake pipeline for quickly running PerSVade's structural variant calling on C auris samples

    Python 0 0 0 0 Updated Jun 17, 2025
  • nanoQC Public

    Quality control pipeline for nanopore long read data

    Python 0 0 0 0 Updated Jun 10, 2025
  • Nanosake Public Forked from alipirani88/Nanosake

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

    Python 0 2 0 0 Updated Jun 6, 2025
  • popSNPkit Public

    Variant calling pipeline for population data

    Python 0 0 0 0 Updated Jun 3, 2025
  • cauris_dotplot Public

    A set of simple scripts for generating synteny dot plots from C auris assemblies

    Python 0 1 0 0 Updated Jun 3, 2025

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