All Published Workflows
993 workflows that have been reviewed and published
![psychip_snakemake](https://media.bioworkflows.com/bioworkflows/public_preview/791b56ccab3630bcb1746d66097f813640394655ed21d3c39cb591b7016d2994.jpg)
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...
![cellranger-snakemake-gke](https://media.bioworkflows.com/bioworkflows/public_preview/1045115046015ac39a849801172555df3b41ec5023f7f7c8230f0640b8f89a2b.jpg)
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](https://media.bioworkflows.com/bioworkflows/public_preview/2e9488df62bdb57adbd8f8a137263f57f970f5571566588f6242d63f73c67151.jpg)
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-star-deseq2](https://media.bioworkflows.com/bioworkflows/public_preview/2b57d357da619c31943bbffc57e2cc955325669933c9b5b91e33b81fd78c18d4.jpg)
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 ...
![dna-seq-gatk-variant-calling](https://media.bioworkflows.com/bioworkflows/public_preview/4b8eed0f6a179f18a43e601e653aee298718468aaf37ee1b3d0f8dddaffcaf6a.jpg)
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...
![armor](https://media.bioworkflows.com/bioworkflows/public_preview/cc7665c55e38e46bd0aba5fbf5b6c09f9be831437a05f091d0e4ec7b56ab42a9.jpg)
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...
![metagem](https://media.bioworkflows.com/bioworkflows/public_preview/9f897d1e5c5be9ea5b04501012110b7aa72e59b8354584eea77e29aa4202b7ae.jpg)
: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...
![v-pipe](https://media.bioworkflows.com/bioworkflows/public_preview/711074687ab0ba435f238465ae19915ac94bb8a0078e32ad735c3188c812096d.jpg)
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...
![pipeline-transcriptome-de](https://media.bioworkflows.com/bioworkflows/public_preview/602f5af232359582918564dd5a4f011be7be53b91e1b71369ede3cf7221c6120.jpg)
Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
This project is deprecated. Please see our newer wf-transcriptomes , which contains functionality for differential exp...
![nanopype](https://media.bioworkflows.com/bioworkflows/public_preview/b2f9dc40c9203873de837f121f13d61ff30419fdd659eb62f656ca95188a11c9.jpg)
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...
![pyflow-chipseq](https://media.bioworkflows.com/bioworkflows/public_preview/f5d0818530af19dd55996539923676f2b46766184a02fac2f955df55637f8f62.jpg)
a snakemake pipeline to process ChIP-seq files from GEO or in-house
a snakemake pipeline to process ChIP-seq files from GEO I have so many people asking me to process a public GEO ChIP-seq data...
![dna-seq-varlociraptor](https://media.bioworkflows.com/bioworkflows/public_preview/d340f005ebb434d0f6a6cb675215dd3df9d4a4e20a9e384a028fcb5cfcf3209d.jpg)
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