All Published Workflows
186 workflows that have been reviewed and published
Pore-C Snakemake Workflow for Processing and Analysis of Nanopore Sequencing Data
This pipeline manages a pore-c workflow starting from raw fastq files and converting them to standard file formats for use by...
Modular Shotgun Sequence Analysis Workflow: Oecophylla - Harnessing Snakemake
Canonically pronounced ee-co-fill-uh , Oecophylla is a Snakemake wrapper for shotgun sequence analysis. Rather than being...
Anvi'o Analysis Workflow Using Snakemake
snakemake rules for running anvio This Snakefile will run a basic anvi'o analysis of a set of assemblies and a set of sam...
Clin-mNGS: Automated pipeline for pathogen detection from clinical metagenomic data
The Clin-mNGS pipeline is an integrated, open-source, scalable, reproducible, and user-friendly framework scripted using the ...
Julia-based Snakemake Workflow for Data Analysis and Document Generation
Fork this repo to easily use Julia in showyourwork . The following modifications were made to the default template (You c...
Single-Cell RNA Sequencing Analysis Workflow Using Drop-seq Tools on SGE Cluster Environment
This pipeline is based on snakemake and the dropseq tools provided by the McCarroll Lab . It starts from raw sequenci...
Parameterized Snakemake Workflows with CLI
An example of parameterizing snakemake workflows with a simple CLI. Usage:
./run <workflow_file> <parameters_file> e.g.
rm -f...
Pharmacogenomics Pipeline using Hydra for WGS Data Analysis
Pharmacogenomics pipeline implemented in hydra To run this workflow, the following tools need to be available:
Add all sa...
Neuroinformatics Workflow for Clinical Atlas Registration and Data Analysis
clinical-atlasreg Inputs:
participants.tsv with target subject IDs
bids folder
other folder containing bids-like ...
Snakemake workflow: species-quantification using kraken2 and bracken
A Snakemake workflow for quantification of species in a sequencing sample, using kraken2 and bracken . Optionally, it...
Single-Cell Transposable Element Analysis Workflow (scTE-snakemake)
Alec Pankow 2022-10-04 A Snakemake workflow for running scTE (single-cell transposable element) quantitation from scRNAse...
Short Tandem Repeat (STR) Catalog Analysis Workflow
Active STRs Analysis This repository contains a Snakemake workflow for analyzing the regulatory and functional role of short ...