All Published Workflows
102 workflows that have been reviewed and published
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
V-pipe is a workflow designed for the analysis of next generation sequencing (NGS) data from viral pathogens. It produces a n...
Snakemake-based workflow for detecting structural variants in genomic data
Structural variants (SVs) are an important class of genetic variation implicated in a wide array of genetic diseases. sv-ca...
Make colorful identity heatmaps of genomic sequence
This is a repository for making colorful identity heatmaps of genomic sequence. To install you can follow the directions on t...
Small collection of tools for performing quality control on coronavirus sequencing data and genomes
Tools and plots for perfoming quality control on coronavirus sequencing results. Download the package:
git clone https://gith...
A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.
A Snakemake workflow to process single samples (unrelated individuals) or cohort samples (related individuals) of paired-end ...
SigMa is a probabilistic model for the sequential dependencies of mutation signatures
This repository contains the source code for SigMa (Signature Markov model) and related experiments. SigMa is a probabilistic...
Neoantigen Prediction Snakemake Workflow: Genomic Variant Detection and Peptidome Incorporation
This workflow detects genomic variants with Strelka and and tries to incorporate germline and somatic variants into a sam...
Sequence
Genetic variation analysis
genetic variants
gatk
hla-la
rust-bio-tools
tabix
Arriba
BCFtools
BWA
Cutadapt
FreeBayes
kallisto
Microphaser
NetMHCIIpan
NetMHCpan
Pandas
Picard
Quant
razers3
SAMtools
Snakemake
STAR
Strelka
Variant Effect Predictor (VEP)
vembrane
Jinja2
numpy
Varlociraptor
Genomics
"DTR Phage Genome Polishing Pipeline"
DTR phage pipeline The DTR phage pipeline is a Snakemake pipeline for obtaining polished, full-length dsDNA bacteriophage gen...
Epidemiological Data Subsampling Pipeline
subsampler A pipeline for subsampling genomic data based on epidemiological time series data. If you use this tool in a publi...
Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
This repo builds on code by Mick Watson who wrote a blog post and follow up about a quick way to test the viabili...
A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets
A Snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB) data (and other custom benchm...
Contamination Detection in the Olive Genome: A Snakemake Workflow on AWS
This workflow includes analyses to find contamination in the domesticated olive genome. The results are presented in this p...