All Published Workflows
251 workflows that have been reviewed and published
![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...
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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
![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/...
![struo](https://media.bioworkflows.com/bioworkflows/public_preview/6c95e47da040bdda2c59dbe9d06ef7d56afa700e826eb6ef10599a14a19093e8.jpg)
![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 ...
![cd4-csaw](https://media.bioworkflows.com/bioworkflows/public_preview/c3fb43f19325460b909d855f597b7fb2d3baf7cd6a2cb5ab8a888cf85f959941.jpg)
Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set
This is the code for a re-analysis of a [GEO dataset][1] that I
originally analyzed for [this paper][2] using statistical met...
BSgenome.Hsapiens.UCSC.hg19
BSgenome.Hsapiens.UCSC.hg38
Gene ID
Peak calling
Quality control report
macs2
ucsc-liftover
BEDTools
BiocParallel
Bowtie 2
csaw
Cufflinks
GenomicAlignments
GenomicRanges
GLUE
graphite
GSEABase
HISAT2
kallisto
Quant
rtracklayer
Salmon
SAMtools
Snakemake
SRAdb
STAR
SummarizedExperiment
assertthat
dplyr
forcats
future
getopt
ggforce
ggplot2
here
ks
magrittr
optparse
reshape2
rex
rlang
scales
stringr
rpy2
rctutils
ChIP-seq
![stag-mwc](https://media.bioworkflows.com/bioworkflows/public_preview/d1aa95ef58e060110d23438f69ce196d8016620c23b2a73a1b07b340a634f0b0.jpg)
StaG Metagenomic Workflow Collaboration
The StaG Metagenomic Workflow Collaboration (mwc) project focuses on providing
a metagenomics analysis workflow suitable for ...
![oecophylla](https://media.bioworkflows.com/bioworkflows/public_preview/a6c58d38076f5b7588be5c85489f5705eb2f396621306c8a054aa6cef1d7bba9.jpg)
Modular Shotgun Sequence Analysis Workflow: Oecophylla - Harnessing Snakemake
Canonically pronounced ee-co-fill-uh , Oecophylla is a Snakemake wrapper for shotgun sequence analysis. Rather than being...
![nbis-meta](https://media.bioworkflows.com/bioworkflows/public_preview/a313d869a5ece3cb72c146dd91f5ddf1cba1017dc12325245ea497335fce687c.jpg)
A snakemake workflow for metagenomic projects
A workflow for metagenomic projects A snakemake workflow for
paired- and/or single-end whole-genome shotgun metagenomic d...
Barrnap
prodigal
MEGAHIT
Biopython
BLAST
Bowtie 2
Centrifuge
CheckM
contigtax
Cutadapt
edgeR
eggNOG-mapper v2
FastANI
FastQC
FeatureCounts
Infernal cmscan (EBI)
kraken2
Krona
MaxBin
MetaBAT 2
metagenomeSeq
MetaPhlAn
metaspades
MultiQC
Pandas
Picard
SAMtools
seqtk
Snakemake
SortMeRNA
SqueezeMeta
Trimmomatic
Trnascan-SE
CONCOCT
common
gtdbtk
networkx
numpy
RGI
![ameta](https://media.bioworkflows.com/bioworkflows/public_preview/69dd01137d0ae012a95788d05e91437b4d97f42b53a32a7ca5c8098cebd5dedf.jpg)
![cuttag-pipeline](https://media.bioworkflows.com/bioworkflows/public_preview/07a6935d8d1643b03df56b67ca4018640c79988e4375325b5496367fcf47a888.jpg)
Pipeline for Cut&Tag analysis
Snakemake pipeline for Cut&Tag analysis
# cd into a project directory
# type the following to get a copy of the pipeline
git ...
![mag_snakemake_wf](https://media.bioworkflows.com/bioworkflows/public_preview/7bb19139c8b1750049fa4c4888ddb2f4ed3444d77957d60fd761282e6ad60aef.jpg)
Recovery of prokaryotic genomes from shotgun metagenomic sequencing data
Overview
System Requirements
Workflow setup
Running pipeline
CPU time
License
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