Published Workflows
Variant calling with OQFE pipeline on cluster systems
This workflow modifies the docker version of the OQFE workflow so that it can be executed on a cluster system using singulari...
ENCODE pipeline for histone marks developed for the psychENCODE project
psychip pipeline is an improved version of the ENCODE pipeline for histone marks developed for the psychENCODE project.
The o...
Near-real time tracking of SARS-CoV-2 in Connecticut
Repository containing scripts to perform near-real time tracking of SARS-CoV-2 in Connecticut using genomic data. This pipeli...
snakemake workflow to run cellranger on a given bucket using gke.
A Snakemake workflow for running cellranger on a given bucket using Google Kubernetes Engine. The usage of this workflow ...
ATLAS - Three commands to start analyzing your metagenome data
Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, t...
raw sequence reads
Genome assembly
Annotation track
checkm2
gunc
prodigal
snakemake-wrapper-utils
MEGAHIT
Atlas
BBMap
Biopython
BioRuby
Bwa-mem2
cd-hit
CheckM
DAS
Diamond
eggNOG-mapper v2
MetaBAT 2
Minimap2
MMseqs
MultiQC
Pandas
Picard
pyfastx
SAMtools
SemiBin
Snakemake
SPAdes
SqueezeMeta
TADpole
VAMB
CONCOCT
ete3
gtdbtk
h5py
networkx
numpy
plotly
psutil
utils
metagenomics
RNA-seq workflow using STAR and DESeq2
This workflow performs a differential gene expression analysis with STAR and Deseq2. The usage of this workflow is described ...
This Snakemake pipeline implements the GATK best-practices workflow
This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
ARMOR ( A utomated R eproducible MO dular R NA-seq) is a Snakemake workflow , aimed at performing a ty...
A SingleCell RNASeq pre-processing snakemake workflow
This pipeline is based on snakemake and the dropseq tools provided by the McCarroll Lab . It allows to go from raw da...
: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
Note An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic inte...