alipirani88

Comparative_Genomics

Micro 612 genomics workshop

snpkit

Modular workflow for Microbial Variant Calling and SNP diagnostics.

samosa

(S)train (A)ssignment from (M)etagen(O)me (S)NP (A)nalysis.

Growth-rate-estimate

Calculate Peak to Trough ratio (PTR) from sequencing data.

QC-d

Generate Coverage, Quality and Contamination metrics for Sequence data.

Comparative_Genomics-V.2.2017

This is an archived repository of 2017 Micro 612 genomics workshop.

find_hgt_pipeline

compare multiple fasta files using nucmer and extract aligned fragments

academic-website

Growth-rate-estimate_SMAKE

Growth-rate-analysis is a Snakemake workflow to calculate peak to through ratio (PTR - ratio of copy numbers at origin of replication to terminus) from mapped reads coverage.

Nanosake

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

QCD_SMAKE

Runs Quality Control workflow on Illumina WGS data

alimohammedpirani

bioconda-recipes

Conda recipes for the bioconda channel.

bioinformatics-coffee-hour

Short lessons from FAS Informatics coffee hour

dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

gatk

Official code repository for GATK versions 4 and up

Perfect-bacterial-genome-tutorial

Plasmid_Detection_in_MRSA_dataset

prewas

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

snakemake_teaser

Getting started with Snakemake workflows for automated bioinformatics analysis.

snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

starter-hugo-academic

🎓 Hugo Academic Theme 创建一个学术网站. Easily create a beautiful academic résumé or educational website using Hugo, GitHub, and Netlify.

StrainEst

Scripts to generate Strainest Database.

varcall_umich

Variant Calling Pipeline

variant_diagnostics

The scripts in this directory analyses various results generated during variant calling analysis and creates diagnostic plots for exploring variants that were filtered out during the variant filteration step. Generates core SNP vcf and consensus file.