All Published Workflows
419 workflows that have been reviewed and published
![ncov_2](https://media.bioworkflows.com/bioworkflows/public_preview/16bd34a67b114b98942f09d5bcfb47c01d0e12aaccac38e15c9bbcc5856d6139.jpg)
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](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
![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...
![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...
![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...
![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
![rna-seq-kallisto-sleuth](https://media.bioworkflows.com/bioworkflows/public_preview/76a6f39480d6ade510201e74d885f132220f55b66883fb76d168379b3cb3bbfd.jpg)
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
![benchpress](https://media.bioworkflows.com/bioworkflows/public_preview/5b6ed57c6af95fc8633da3dca7d7504221eaa4a6a7fa3d7768ca76076f82e388.jpg)
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...
![phanta](https://media.bioworkflows.com/bioworkflows/public_preview/60692bead9908136ac0585a7289753a9ce303a8e989c51d923fca58fa9948924.jpg)
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 ...
![tourmaline](https://media.bioworkflows.com/bioworkflows/public_preview/ba7e9ae8b3c64d065e3767a7ce62f497c0f91725ac3ebac47bd87c577f80243f.jpg)
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...
![natrix](https://media.bioworkflows.com/bioworkflows/public_preview/e869c6522fdc626f4352051ec23940335655df117c2d7043aaa2d8b10f40a115.jpg)
Open-source bioinformatics pipeline for the preprocessing of raw sequencing data.
Natrix is an open-source bioinformatics pipeline for the preprocessing of raw sequencing data.
The need for a scalable, repro...
![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 ...