A reproducible Snakemake pipeline to analyse Illumina paired-end data from ChiP-Seq experiments
A reproducible Snakemake pipeline to analyse Illumina paired-end data from ChiP-Seq experiments - Published in JOSS (2019)
catd_snakemake
Snakemake pipeline for benchmarking cell-type deconvolution methods and deconvolving real bulk RNA-seq data with the use of scRNA-seq datasets
snakemake-workflow-fermi-lat
A Snakemake workflow for Fermi-LAT data reduction
metagem
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
dea_limma
A Snakemake workflow and MrBiomics module for performing and visualizing differential (expression) analyses (DEA) on NGS data powered by the R package limma.
spilterlize_integrate
A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.
mixscape_seurat
A Snakemake workflow and MrBiomics module for performing perturbation analyses of pooled (multimodal) CRISPR screens with sc/snRNA-seq read-out (scCRISPR-seq) powered by the R package Seurat's method Mixscape.
dea_seurat
A Snakemake workflow and MrBiomics module for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.
euryale
A pipeline for taxonomic classification and functional annotation of metagenomic reads. Based on MEDUSA
snhic
Snakemake pipeline for analysis and normalization of Hi-C data starting from fastq.gz files. It includes the possibility to perform grouped analyses, TAD, loops and stripes detections, as well as differential compartment and chromatin interaction analyses.
snakemake
This is the development home of the workflow management system Snakemake. For general information, see
metagenome-atlas
ATLAS - Three commands to start analyzing your metagenome data
vipera
A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis
transcluster
A Snakemake workflow to find SARS-CoV-2 clusters in a reference phylogeny and estimate their normalized clustering index
scanneo2
Snakemake-based computational workflow for neoantigen prediction from diverse sources
unsupervised_analysis
A general purpose Snakemake workflow and MrBiomics module to perform unsupervised analyses (dimensionality reduction & cluster analysis) and visualizations of high-dimensional data.
https://github.com/adonath/snakemake-workflow-chandra
A Snakemake workflow for Chandra data reduction
solar-and-wind-potentials
Estimation of solar and wind power generation potentials in Europe.
https://github.com/cbg-ethz/v-pipe
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
https://github.com/cbg-ethz/pybda
:computer::computer::computer: A commandline tool for analysis of big biological data sets for distributed HPC clusters.
https://github.com/biocore/qadabra
Snakemake workflow for comparison of differential abundance ranks
https://github.com/cbg-ethz/sars-cov-2_analysis
A Snakemake workflow for large-scale SARS-CoV-2 analyses.
tucca-rna-seq
Tufts University Center for Cellular Agriculture's RNA-Seq Workflow for Cellular Agriculture Projects
enrichment_analysis
A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.
spikeflow
Pipeline to analyse ChIP-Rx data, i.e ChIP-Seq with reference exogenous genome spike-in normalization
population-structural-var-calling-smoove
population structural variant calling with smoove
rnaseq_pipeline
RNA-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
megaisurv-namaste
Nanopore Metagenomic Antibiotic Resistance and Taxonomy Screening
sv-callers
Snakemake-based workflow for detecting structural variants in genomic data
https://github.com/cbg-ethz/scdna-pipe
Python data analysis pipeline for single cell copy number event history reconstruction
https://github.com/clavellab/genome-assembly
A Snakemake workflow assembling bacterial genomes according to the standard operating procedure in the Clavel Lab
atacseq_pipeline
Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
sv-gen
Snakemake-based workflow for generating artificial genomes with structural variants
fair_bowtie2_mapping
Align reads over a reference genome, filter aligned-reads, and mark duplicates
snakemake_rnaseq
A Snakemake pipeline to go from fastq mRNA sequencing files to raw and normalised counts (usable for downstream EDA and differential analysis)
popglen
Bioinformatics pipeline to process whole genome resequencing data and perform genotype likelihood based population genomic analyses using ANGSD and related softwares. Flexible to datasets that combine high/low coverage and historical/fresh samples.
genome_tracks
A Snakemake workflow and MrBiomics module for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq, scRNA-seq, ...) powered by the wrapper gtracks for the package pyGenomeTracks, and IGV-reports.
snakemake-publishing
Lessons on taking a basic Snakemake workflow and sharing it with the community
cnakepit
A Snakemake pipeline for copy number variant calling without normal tissue samples
zarp-cli
A user-friendly command-line interface for the ZARP RNA-seq analysis workflow
rdscan
A snakemake workflow for regions of difference discovery in Mycobacterium tuberculosis complex (MTBC) samples
fair_genome_indexer
Download and index Ensembl sequences and annotations, remove non-canonical chromosimes, remove low TSL, index with multiple tools
viroconstrictor
ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences of the given viral genome
grenepipe
A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - for sampled individuals, and for pool sequencing.
mpox-seek
A rapid pipeline for targeted and whole-genome ONT monkeypox sequencing
fair_gatk_mutect2
Snakemake workflow used to call germline and/or somatic variants with GATK Mutect2
ena-spike-ntd-repdel-analysis
A Snakemake workflow with associated scripts used for detecting spike NTD repaired deletions in SARS-CoV-2 Omicron BA.1 lineage reads. Manuscript under review.
rna-seq-salmon-deseq2
Snakemake workflow for RNA-Seq differential transcript analysis using Salmon/Deseq2
https://github.com/angrymaciek/warlock
Warlock is a snakemake workflow to spawn multiple demons (deme-based oncology models) as jobs running around on a cluster environment 😈😈
https://github.com/angrymaciek/mapp
🗺️ MAPP is a computational method which enables identification of binding motifs for RNA-binding proteins that shape pre-mRNA processing under specific conditions.
pypsa-eur
PyPSA-Eur: A Sector-Coupled Open Optimisation Model of the European Energy System
https://github.com/charlesfoster/mitowrap
A snakemake pipeline wrapping MitoZ and getOrganelle for de novo mitogenome assembly using short reads and subsequent QC.
https://github.com/ccbr/ccbr_snakemaketemplate
Barebones framework for creating new snakemake workflows.
snakemake-novice-lattice
Introduction to Snakemake for Lattice Quantum Field Theory
scrnaseq_processing_seurat
A Snakemake workflow and MrBiomics module for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX matrix file format powered by the R package Seurat.