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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

  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 40 repositories
  • caurisblast Public

    Python scripts to assist with BLASTing sequences from Candida auris

    Snitkin-Lab-Umich/caurisblast’s past year of commit activity
    Python 0 0 0 0 Updated Mar 29, 2025
  • Snitkin-Lab-Umich/EPID582-Winter-2025’s past year of commit activity
    HTML 1 0 3 0 Updated Mar 26, 2025
  • cauris_dotplot Public

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

    Snitkin-Lab-Umich/cauris_dotplot’s past year of commit activity
    Python 0 0 0 0 Updated Mar 25, 2025
  • 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 Mar 21, 2025
  • 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 Mar 15, 2025
  • nanofunsake Public

    A pipeline for hybrid assembly, QC, and annotation of C auris genomes

    Snitkin-Lab-Umich/nanofunsake’s past year of commit activity
    Python 0 0 0 0 Updated Mar 14, 2025
  • QCD Public

    Runs Quality Control workflow on Illumina WGS data

    Snitkin-Lab-Umich/QCD’s past year of commit activity
    Python 2 2 6 1 Updated Mar 13, 2025
  • nanofunQC Public

    QC and annotation pipeline for C auris nanopore sequencing data

    Snitkin-Lab-Umich/nanofunQC’s past year of commit activity
    Python 0 0 0 0 Updated Mar 7, 2025
  • phylokit Public

    Snakemake pipeline to generate a phylogenetic tree from an alignment

    Snitkin-Lab-Umich/phylokit’s past year of commit activity
    Python 0 0 1 0 Updated Feb 27, 2025
  • 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 2 MIT 5 0 0 Updated Feb 21, 2025

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