All Published Workflows

3 workflows that have been reviewed and published

dropseqpipe
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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
iguide
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Bioinformatic pipeline for identifying dsDNA breaks by marker based incorporation, such as breaks induced by designer nucleases like Cas9.
public

public

Bioinformatic pipeline for processing iGUIDE and GUIDE-seq samples. iGUIDE is a pipeline written in snakemake for proc...
Data Read pre-processing Report Biostrings BSgenome BWA Quant SAMtools Snakemake magrittr DNA
Free
65
gatk4-data-processing
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Snakemake implementation of data pre-processing for variant discovery from GATK Best Practices Workflows
public

public

Snakemake implementation of data pre-processing for variant discovery from GATK Best Practices Workflows
Data Read pre-processing genetic variants gatk BWA SAMtools Snakemake Data identity and mapping
Free
7