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@Snitkin-Lab-Umich

Snitkin-Lab-Umich

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  1. prewas prewas Public

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

    R 5 3

  2. hogwash hogwash Public

    Forked from katiesaund/hogwash

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

    R 1 1

  3. cognac cognac Public

    Forked from rdcrawford/cognac

    cognac: COre GeNe Alignment Concatenation

    C++ 1

  4. snitkitr snitkitr Public

    common R functions used in the lab

    R 1 1

  5. regentrans regentrans Public

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

    R 5 1

  6. Comparative_Genomics Comparative_Genomics Public

    Forked from alipirani88/Comparative_Genomics

    Microbial Bioinformatics Workshop

    Shell 1 1

Repositories

Showing 10 of 54 repositories
  • NG-probe Public

    A Snakemake pipeline for culture-free Neisseria gonorrhoeae genome reconstruction and detection of putative resistance determinants from probe-based genomic sequencing.

    Snitkin-Lab-Umich/NG-probe's past year of commit activity
    Python 1 0 0 0 Updated Sep 8, 2026
  • phylokit Public

    Snakemake pipeline to generate a phylogenetic tree from an alignment

    Snitkin-Lab-Umich/phylokit's past year of commit activity
    Python 0 1 0 0 Updated Aug 31, 2026
  • QCD Public

    Runs Quality Control workflow on Illumina WGS data

    Snitkin-Lab-Umich/QCD's past year of commit activity
    Python 5 2 4 1 Updated Aug 21, 2026
  • snpkit Public Forked from alipirani88/snpkit

    Active version of snpkit, a Modular/Scalable workflow for Microbial Variant Calling, Recombination detection and Phylogenetic tree reconstruction.

    Snitkin-Lab-Umich/snpkit's past year of commit activity
    Python 3 MIT 5 2 0 Updated Aug 21, 2026
  • pangenome_blast_smk Public

    A snakemake pipeline for comparing Panaroo pangenome results against a BLAST search

    Snitkin-Lab-Umich/pangenome_blast_smk's past year of commit activity
    Python 0 0 0 0 Updated Aug 17, 2026
  • cauris_panaroo Public

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

    Snitkin-Lab-Umich/cauris_panaroo's past year of commit activity
    Python 0 0 0 0 Updated Aug 17, 2026
  • treereduce Public

    python scripts for subsetting newick trees based on SNP distance

    Snitkin-Lab-Umich/treereduce's past year of commit activity
    Python 0 0 0 0 Updated Aug 17, 2026
  • cauris-data-flow Public

    data flow scripts for C auris sequencing

    Snitkin-Lab-Umich/cauris-data-flow's past year of commit activity
    Python 0 0 0 0 Updated Jul 31, 2026
  • funQCD Public

    Quality control pipeline for short read fungal data

    Snitkin-Lab-Umich/funQCD's past year of commit activity
    Python 0 0 0 0 Updated Jul 31, 2026
  • pubQCD Public

    Quality control pipeline for datasets downloaded from public databases

    Snitkin-Lab-Umich/pubQCD's past year of commit activity
    Python 1 0 0 0 Updated Jul 14, 2026

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