All Published Workflows
292 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 ...
![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...
![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
![stainedglass](https://media.bioworkflows.com/bioworkflows/public_preview/806d018c3cb232f52b73e59ded90b880e1dde535430b4937b7c55abda2eade05.jpg)
Make colorful identity heatmaps of genomic sequence
This is a repository for making colorful identity heatmaps of genomic sequence. To install you can follow the directions on t...
![pyflow-atacseq](https://media.bioworkflows.com/bioworkflows/public_preview/0427548c3d2793ad7c678c3d0ae7b4d42f5a83f03b324149205546fd86f6b6e8.jpg)
ATAC-seq snakemake pipeline
source: http://www.the-scientist.com/?articles.view/articleNo/44772/title/Reveling-in-the-Revealed/ https://www.biostars.org/...
![lathe](https://media.bioworkflows.com/bioworkflows/public_preview/1f180f3eaf10aa1f49825688bd4634606b3e4c92a2d6c655dd34486bf7715039.jpg)
A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
A tool for generating bacterial genomes from metagenomes with Nanopore long read sequencing First, install miniconda3 The...
![ncov-tools](https://media.bioworkflows.com/bioworkflows/public_preview/b1dff15df91343052a01e1cf42ef3bd673f88509e074d6425e7d990fd18b7fa7.jpg)
Small collection of tools for performing quality control on coronavirus sequencing data and genomes
Tools and plots for perfoming quality control on coronavirus sequencing results. Download the package:
git clone https://gith...
![covid-19-signal](https://media.bioworkflows.com/bioworkflows/public_preview/654963db437af051ec1197e3ab2a3eb4c6cbdc09928cdc2b32ea2aa3d58d2787.jpg)
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
This is a complete standardized workflow the assembly and subsequent analysis for short-read viral sequencing.
This core work...
![mapache](https://media.bioworkflows.com/bioworkflows/public_preview/bb656e17ac94b23426305db1b39bff6177b185cdd574346d96093c6f5281264c.jpg)
mapping pipeline for ancient DNA
Mapache ([maˈpa.t͡ʃe]) is a lightweight mapping pipeline for ancient DNA using the workflow manager Snakemake . Visit ...