snitkin-lab-umich Goto Github PK

ariba_snakemake

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

assemblage

Microbial Genome Assembly Pipeline

beast

code_club_curriculum

Curriculum for the Snitkin Lab Code Clubs

cognac

cognac: COre GeNe Alignment Concatenation

comparative_genomics

Microbial Bioinformatics Workshop

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

genome_downloading_snakemake

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

hogwash

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

ltach-crkp-colistin-ms

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

micro582-epi582-winter-2024

MICRO582/EPI582 - Genomic Epidemiology Winter Course 2022

ml-crkp-infection-manuscript

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

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

prewas

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

prewas_manuscript_analysis

Manuscript in support of prewas software

qc-d

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

qcd

Runs Quality Control workflow on Illumina WGS data

regentrans

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

sample_snakemake

Example snakemake pipeline

scripts

Frequently used Scripts

snakemake_setup

Setup information for snakemake pipelines

snitkitr

common R functions used in the lab

snpkit

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

snpkit-smk

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

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)