All Published Workflows
103 workflows that have been reviewed and published
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...
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
Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.
A reproducible and scalable workflow for transparent and robust SARS-CoV-2
variant calling and lineage assignment with com...
JSON
raw sequence reads
Variant calling
genetic variants
delly
nanofilt
rust-bio-tools
snakemake-wrapper-utils
tabix
BCFtools
Biopython
BWA
CANU
Consensus
fastp
FastQC
fgbio
FreeBayes
GFFutils
kallisto
Kraken
Krona
Medaka
metaspades
Minimap2
MultiQC
Pandas
Pangolin
Picard
Quant
QUAST
SAMtools
Snakemake
Variant Effect Predictor (VEP)
vembrane
altair
intervaltree
numpy
pysam
requests
Varlociraptor
COVID19 Risk Mitigation
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
Documentation : https://sanjaynagi.github.io/rna-seq-pop/
Walkthrough : https://www.youtube.com/watch?v=5QQe7DLHO4...
FASTQ-illumina
JSON
Sample annotation
Variant calling
genetic variants
snakemake-wrapper-utils
EnhancedVolcano
BCFtools
DESeq2
fastp
FreeBayes
GLUE
HISAT2
kallisto
mosdepth
MultiQC
Pandas
pheatmap
Quant
SAMBLASTER
SAMtools
sleuth
Snakemake
snpEff
Vcflib
data.table
dplyr
ggplot2
ggrepel
jsonlite
openxlsx
RColorBrewer
tidyverse
ipykernel
matplotlib
matplotlib-venn
numpy
papermill
pop-tools
scipy
zarr
Population genomics
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
A modular, flexible, and reproducible Snakemake workflow to perform k-mers-based GWAS.
Summary
Installation
...
Snakemake workflow for somatic mutation detection without matched normal samples
TOSCA ( T umor O nly S omatic CA lling) is a Snakemake workflow , aimed at performing a somatic varian...
A repo for the Twist HiFi capture/snakemake workflow
This is a snakemake workflow for analyzing targeted HiFi sequence datasets. The workflow was designed for Twist gene pane...
Pipeline to pull microbial reads from WGS data and perform metagenomic analysis
Doi for manuscript: https://doi.org/10.12688/wellcomeopenres.19155.1 Please follow the tutorial in my Jupyter Book Available ...
A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets
A Snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB) data (and other custom benchm...