All Published Workflows

2456 workflows that have been reviewed and published

psychip_snakemake
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ENCODE pipeline for histone marks developed for the psychENCODE project
public

public

psychip pipeline is an improved version of the ENCODE pipeline for histone marks developed for the psychENCODE project. The o...
raw sequence reads Alignment Sequence alignment report macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74 0(0)
ncov_2
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Near-real time tracking of SARS-CoV-2 in Connecticut
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public

Repository containing scripts to perform near-real time tracking of SARS-CoV-2 in Connecticut using genomic data. This pipeli...
JSON nextclade Augur Biopython FOCUS Pandas Snakemake bs4 epiweeks geopy matplotlib numpy pycountry pycountry-convert uszipcode
Free
28 0(0)
cellranger-snakemake-gke
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snakemake workflow to run cellranger on a given bucket using gke.
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public

A Snakemake workflow for running cellranger on a given bucket using Google Kubernetes Engine. The usage of this workflow ...
macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74 0(0)
atlas
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ATLAS - Three commands to start analyzing your metagenome data
public

public

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
Free
175 0(0)
rna-seq-star-deseq2
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RNA-seq workflow using STAR and DESeq2
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public

This workflow performs a differential gene expression analysis with STAR and Deseq2. The usage of this workflow is described ...
raw sequence reads Gene expression profiling ID list snakemake-wrapper-utils biomaRt PCAtools BiocParallel BWA Cutadapt DESeq2 GFFutils MultiQC Pandas SAMtools Snakemake STAR cli stringr tidyverse RNA-Seq
Free
41 0(0)
dna-seq-gatk-variant-calling
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This Snakemake pipeline implements the GATK best-practices workflow
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public

This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
VCF raw sequence reads Variant calling genetic variants gatk rust-bio-tools snakemake-wrapper-utils tabix BCFtools BWA FastQC MultiQC Pandas Picard SAMtools Snakemake Trimmomatic Variant Effect Predictor (VEP) common matplotlib numpy seaborn DNA
Free
57 0(0)
armor
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Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
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public

ARMOR ( A utomated R eproducible MO dular R NA-seq) is a Snakemake workflow , aimed at performing a ty...
JSON User metadata Expression analysis Quality control report bedGraphToBigWig BEDTools Cutadapt FastQC MultiQC Quant Salmon SAMtools Snakemake STAR Trim_Galore RNA-Seq
Free
22 0(0)
dropseqpipe
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A SingleCell RNASeq pre-processing snakemake workflow
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public

This pipeline is based on snakemake and the dropseq tools provided by the McCarroll Lab . It allows to go from raw da...
raw sequence reads Read pre-processing Report umi_tools BBMap Biopython Cutadapt FastQC MultiQC Seurat Snakemake STAR devtools dplyr ggplot2 gridExtra Matrix plotly plyr RColorBrewer stringr tidyr viridis yaml pysam scRNAseq data processing
Free
82 0(0)
metagem
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: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
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Note An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic inte...
JSON raw sequence reads Genome assembly Quality control report prodigal MEGAHIT BWA CheckM fastp kallisto MaxBin memote MetaBAT 2 metaprokka MetaWRAP Quant Roary SAMtools Snakemake SqueezeMeta CONCOCT carve gtdbtk smetana metagenomics
Free
35 0(0)
v-pipe
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V-pipe is a pipeline designed for analysing NGS data of short viral genomes
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public

V-pipe is a workflow designed for the analysis of next generation sequencing (NGS) data from viral pathogens. It produces a n...
Sample annotation Primer removal Quality control report bcl2fastq-nextseq consensusfixer demultiplexer indelfixer Augur BWA Consensus iVar lofreq Pandas SAMtools Snakemake Vicuna numpy PyVCF scikit-bio scipy Genomics
Free
68 0(0)
pipeline-transcriptome-de
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Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
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public

This project is deprecated. Please see our newer wf-transcriptomes , which contains functionality for differential exp...
FASTQ Sample ID Alignment Count matrix Minimap2 Quant Salmon SAMtools Snakemake stageR dplyr ggplot2 tidyr Gene expression
Free
14 0(0)
single-cell-rna-seq
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A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.
public

public

A single cell RNA-seq workflow following Lun, McCarthy and Marioni 2016 and Soneson and Robinson 2018 , with added mo...
PCAtools CellAssign ComplexHeatmap edgeR limma RBGL Rgraphviz scater scran SingleCellExperiment TensorFlow dplyr ggplot2 ggpubr ggsci gplots RColorBrewer tidyverse viridis
Free
40 0(0)