All Published Workflows
622 workflows that have been reviewed and published
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...
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...
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 pipelines for nanopore sequencing data archiving and processing
Detailed documentation and tutorials are available at readthedocs . Nanopype is a snakemake based pipeline providing conv...
A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse...
JSON
raw sequence reads
Variant calling
genetic variants
delly
gatk
rust-bio-tools
snakemake-wrapper-utils
tabix
BCFtools
BEDTools
Bowtie 2
BWA
Cutadapt
FastQC
fgbio
FreeBayes
mosdepth
MultiQC
Pandas
Picard
SAMtools
Snakemake
Variant Effect Predictor (VEP)
vembrane
numpy
oschmod
sklearn
statsmodels
Varlociraptor
DNA
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth . The usage of thi...
JSON
Expression data
Expression analysis
Expression data
bioawk
snakemake-wrapper-utils
biomaRt
IHW
Biopython
BWA
CPAT
Cutadapt
fgsea
graphite
GSEA
IsoformSwitchAnalyzeR
kallisto
limma
Pandas
pheatmap
Picard
Quant
SAMtools
sleuth
Snakemake
SPIA
dplyr
fs
ggplot2
ggpubr
gridExtra
tidyr
tidyverse
altair
altair-saver
goatools
matplotlib
numpy
pysam
scipy
RNA-Seq
Snakemake workflow for metagenomic classification with Kraken2
A Snakemake pipeline wrapper of the Kraken2 short read metagenomic classification software, with additional tools for analysi...
A Snakemake workflow to run and benchmark structure learning (a.k.a. causal discovery) algorithms for probabilistic graphical models.
Benchpress [1] is a Snakemake workflow where structure learning algorithms, implemented in possibly different lang...
Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
Workflow figure created on BioRender.com. Pinto, Y., Chakraborty, M., Jain, N. et al. Phage-inclusive profiling of human gut ...
Amplicon sequence processing workflow using QIIME 2 and Snakemake
Tourmaline is an amplicon sequence processing workflow for Illumina sequence data that uses QIIME 2 and the software pack...