Snitkin-Lab-Umich

prewas

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

regentrans

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

MICRO582-EPI582-Winter-2024

MICRO582/EPI582 - Genomic Epidemiology Winter Course 2022

genome_downloading_snakemake

Snakemake pipeline to download genomes from NCBI using Biosample Accession Numbers and fasterq-dump

scripts

Frequently used Scripts

snpkit

A Modular/Scalable workflow for Microbial Variant Calling, Recombination detection and Phylogenetic tree reconstruction.

beast

cognac

cognac: COre GeNe Alignment Concatenation

Comparative_Genomics

Microbial Bioinformatics Workshop

ml-crkp-infection-manuscript

Code and some data related to manuscript on machine learning to study CRKP colonization and infection

prewas_manuscript_analysis

Manuscript in support of prewas software

QCD

Runs Quality Control workflow on Illumina WGS data

snitkitr

common R functions used in the lab

assemblage

Microbial Genome Assembly Pipeline

code_club_curriculum

Curriculum for the Snitkin Lab Code Clubs

hogwash

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

snpkit-smk

Snakemake workflow for Microbial Variant Calling, Recombination detection and Phylogenetic tree reconstruction.

ariba_snakemake

Snakemake pipeline to run ARIBA on genomes using CARD, PlasmidFinder, or MLST database

data-carpentry-genomics

Instructor notes for Data Carpentry for genomics 2-day workshop

eip-cre-transmission-ms

Code and data related to EIP CRE transmission project

ltach-crkp-colistin-ms

Data, code, and figures corresponding to LTACH CRKP colistin manuscript

Nanosake

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

ndm-st147-chicago-ms

Code related to manuscript: Regional spread of blaNDM-1-containing Klebsiella pneumoniae Sequence Type 147 in post-acute care facilities

QC-d

calculate sequencing coverage and read depth, assess read quality and detect contamination

sample_snakemake

Example snakemake pipeline

Snakemake_setup

Setup information for snakemake pipelines

Topcuoglu_ML_XXX_2019

Best practices for applying machine learning to bacterial 16S rRNA gene sequencing data

UnitTestsAndFunctionChecks

UnitTestsAndFunctionChecks

varcall_umich

Variant Calling Pipeline(Deprecated)