All Published Workflows

105 workflows that have been reviewed and published

dropseqpipe
Show Details View Workflow
A SingleCell RNASeq pre-processing snakemake workflow
public

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
rna-seq-kallisto-sleuth
Show Details View Workflow
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
public

public

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
Free
105
lathe
Show Details View Workflow
A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
public

public

A tool for generating bacterial genomes from metagenomes with Nanopore long read sequencing First, install miniconda3 The...
bacterial Base-calling Sample annotation mummer2circos tabix BCFtools BEDTools BWA CANU Consensus Flye GUPPY Medaka Minimap2 NanoPlot pilon Racon SAMtools Snakemake pysam metagenomics
Free
39
varca
Show Details View Workflow
Use an ensemble of variant callers to call variants from ATAC-seq data
public

public

A pipeline for running an ensemble of variant callers to predict variants from ATAC-seq reads. The entire pipeline is made up...
VCF Data Variant calling genetic variants delly macs2 tabix BCFtools BEDTools BWA Pandas SAMtools Snakemake BBmisc data.table dplyr ggplot2 parallelMap plyr R.devices matplotlib numpy pysam sklearn ATAC-seq deep learning
Free
39
uncovar
Show Details View Workflow
Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.
public

public

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
Free
204
chipseq
Show Details View Workflow
ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).
public

public

This is the template for a new Snakemake workflow. Replace this text with a comprehensive description covering the purpose an...
Data Peak calling Quality control report bedGraphToBigWig BEDTools BiocParallel BWA Cutadapt DESeq2 FastQC FeatureCounts GFFutils homer MaCS MultiQC Pandas pheatmap Picard SAMtools Snakemake UpSetR vsn ggplot2 lattice optparse RColorBrewer reshape2 scales tidyverse pysam PyYAML smart-open ChIP-seq
Free
117
mosaicatcher-pipeline
Show Details View Workflow
Integrated workflow for SV calling from single-cell Strand-seq data
public

public

Structural variant calling from single-cell Strand-seq data Snakemake pipeline. This workflow uses Snakemake to execu...
mosaicatcher tabix BCFtools BEDTools ComplexHeatmap Pandas pheatmap SAMtools Snakemake TensorFlow WhatsHap assertthat BiocManager cowplot data.table devtools dplyr ggnewscale ggplot2 ggpubr matrixStats optparse RColorBrewer reshape reshape2 scales stringr tibble tidyr intervaltree matplotlib numpy parmap plotly pysam PyYAML scipy seaborn tqdm xopen
Free
202
haplotyped-methylome
Show Details View Workflow
Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation
public

public

Reproducibility instructions for Gigante et al., 2019. Note: this repository is still being tested! If you find a bug, plea...
snpsplit Biopython bsseq BWA DSS GenomicRanges HISAT2 nanopolish SAMtools Snakemake Bismark broom data.table dplyr magrittr readr tidyverse numpy pysam Trim_Galore
Free
116
pyflow-scatacseq
Show Details View Workflow
snakemake workflow for post-processing scATACseq data
public

public

snakemake workflow for post-processing scATACseq data cite if you use it:) for single cell ATACseq experiment, one gets a mer...
genrich BEDTools DeepTools pRESTO SAMtools Seurat Snakemake docopt Matrix tidyverse pysam
Free
22
kgwasflow
Show Details View Workflow
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
public

public

A modular, flexible, and reproducible Snakemake workflow to perform k-mers-based GWAS. Summary Installation ...
snakemake-wrapper-utils tabix BEDTools BLAST Bowtie 2 Cutadapt FastQC KMC Minimap2 MultiQC Pandas SAMtools seqkit Snakemake SPAdes matplotlib natsort numpy pysam qmplot scipy seaborn
Free
85
lathe
Show Details View Workflow
A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
public

public

A tool for generating bacterial genomes from metagenomes with Nanopore long read sequencing First, install miniconda3 The...
mummer2circos tabix BCFtools BEDTools BWA CANU Consensus Flye GUPPY Medaka Minimap2 NanoPlot pilon Racon SAMtools Snakemake pysam
Free
37
hemomips
Show Details View Workflow
Automated analysis and result reporting for targeted sequencing data
public

public

The hemoMIPs pipeline is a fast and efficient analysis pipeline for the analysis of multiplexed and targeted NGS datasets cre...
gatk tabix BEDTools BWA SAMtools Snakemake Variant Effect Predictor (VEP) pysam
Free
33