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    36 repositories

    • EPID582-Winter-2025

      Public
      HTML
      •0•1•2•0•Updated Jan 25, 2025Jan 25, 2025

    • QCD

      Public
      Runs Quality Control workflow on Illumina WGS data
      Python
      •2•1•1•1•Updated Jan 23, 2025Jan 23, 2025

    • Data-Flow-SOP

      Public
      SOPs for processing short, long, and hybrid bacterial data
      Python
      •0•0•0•0•Updated Jan 21, 2025Jan 21, 2025

    • snpkit

      Public
      Active version of snpkit, a Modular/Scalable workflow for Microbial Variant Calling, Recombination detection and Phylogenetic tree reconstruction.
      active-repopreferred
      Python
      •
      MIT License
      •5•2•1•0•Updated Jan 17, 2025Jan 17, 2025

    • nanofunQC

      Public
      QC and annotation pipeline for C auris nanopore sequencing data
      Python
      •0•0•0•0•Updated Jan 2, 2025Jan 2, 2025

    • funQCD

      Public
      Quality control pipeline for short read fungal data
      Python
      •0•0•0•0•Updated Jan 2, 2025Jan 2, 2025

    • nanofunsake

      Public
      A pipeline for hybrid assembly, QC, and annotation of C auris genomes
      Python
      •0•0•0•0•Updated Jan 1, 2025Jan 1, 2025

    • snpkit-smk

      Public
      Snakemake workflow for Microbial Variant Calling, Recombination detection and Phylogenetic tree reconstruction.
      Python
      •0•0•5•0•Updated Nov 18, 2024Nov 18, 2024

    • nanoQC

      Public
      Quality control pipeline for nanopore long read data
      Python
      •0•0•0•0•Updated Aug 27, 2024Aug 27, 2024

    • Anaerobe-genomics-workshop

      Public
      0•0•0•0•Updated Jul 6, 2024Jul 6, 2024

    • Nanosake

      Public
      A Snakemake workflow to basecall, quality control and assemble Nanopore data.
      Python
      •2•0•0•0•Updated May 28, 2024May 28, 2024

    • MICRO582-EPI582-Winter-2024

      Public
      MICRO582/EPI582 - Genomic Epidemiology Winter Course 2022
      HTML
      •1•3•1•0•Updated Apr 3, 2024Apr 3, 2024

    • eip-cre-transmission-ms

      Public
      Code and data related to EIP CRE transmission project
      HTML
      •
      MIT License
      •0•0•0•0•Updated Aug 3, 2023Aug 3, 2023

    • ltach-crkp-colistin-ms

      Public
      Data, code, and figures corresponding to LTACH CRKP colistin manuscript
      Other
      •0•0•0•0•Updated May 21, 2023May 21, 2023

    • prewas

      Public
      R package to perform data pre-processing for more informative bacterial GWAS
      gwasrmicrobiologyr-packagebacterial-genomesgwas-tools
      R
      •
      Other
      •3•5•8•0•Updated Apr 7, 2023Apr 7, 2023

    • regentrans

      Public
      regentrans: R package for investigating regional pathogen transmission using genomic data
      R
      •
      Other
      •1•5•9•0•Updated Jan 23, 2023Jan 23, 2023

    • code_club_curriculum

      Public
      Curriculum for the Snitkin Lab Code Clubs
      HTML
      •2•0•0•0•Updated Jun 13, 2022Jun 13, 2022

    • ndm-st147-chicago-ms

      Public
      Code related to manuscript: Regional spread of blaNDM-1-containing Klebsiella pneumoniae Sequence Type 147 in post-acute care facilities
      Other
      •0•0•0•0•Updated Feb 14, 2022Feb 14, 2022

    • ml-crkp-infection-manuscript

      Public
      Code and some data related to manuscript on machine learning to study CRKP colonization and infection
      R
      •
      MIT License
      •1•1•0•0•Updated Jun 10, 2021Jun 10, 2021

    • hogwash

      Public
      Three bacterial GWAS methods all rolled into one easy-to-use R package
      R
      •
      Other
      •5•0•0•0•Updated May 28, 2021May 28, 2021

    • snitkitr

      Public
      common R functions used in the lab
      R
      •
      Other
      •1•1•2•0•Updated Apr 20, 2021Apr 20, 2021

    • cognac

      Public
      cognac: COre GeNe Alignment Concatenation
      C++
      •2•1•0•0•Updated Apr 6, 2021Apr 6, 2021

    • data-carpentry-genomics

      Public
      Instructor notes for Data Carpentry for genomics 2-day workshop
      R
      •0•0•0•0•Updated Mar 18, 2021Mar 18, 2021

    • assemblage

      Public
      Microbial Genome Assembly Pipeline
      Python
      •1•0•0•0•Updated Feb 18, 2021Feb 18, 2021

    • ariba_snakemake

      Public
      Snakemake pipeline to run ARIBA on genomes using CARD, PlasmidFinder, or MLST database
      Shell
      •1•0•0•0•Updated Sep 8, 2020Sep 8, 2020

    • genome_downloading_snakemake

      Public
      Snakemake pipeline to download genomes from NCBI using Biosample Accession Numbers and fasterq-dump
      R
      •0•2•0•0•Updated Jul 22, 2020Jul 22, 2020

    • Snakemake_setup

      Public
      Setup information for snakemake pipelines
      0•0•0•0•Updated Jul 22, 2020Jul 22, 2020

    • QC-d

      Public
      calculate sequencing coverage and read depth, assess read quality and detect contamination
      Python
      •2•0•0•0•Updated Jul 16, 2020Jul 16, 2020

    • scripts

      Public
      Frequently used Scripts
      Perl
      •1•2•15•0•Updated Jul 7, 2020Jul 7, 2020

    • sample_snakemake

      Public
      Example snakemake pipeline
      R
      •1•0•0•0•Updated May 14, 2020May 14, 2020