All Published Workflows

14 workflows that have been reviewed and published

quaich
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snakemake pipeline for Hi-C post-processing
public

public

Quaich is a snakemake based workflow for reproducible and flexible analysis of Hi-C data. Quaich uses multi-resolu...
bigWig Sample annotation cis-regulatory element prediction Plot cooltools Snakemake Data architecture, analysis and design
Free
29
tapseq_manuscript
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Analysis code for the TAP-seq manuscript.
public

public

This repository contains code to reproduce the results presented in the article. It builds upon a snakemake workflow that...
bigWig ucsc-liftover BiocParallel Biopython Biostrings BSgenome Consensus GenomicAlignments GenomicFeatures GenomicRanges HiTC Pandas Picard rtracklayer SAMtools Snakemake STAR Trimmomatic corrplot eulerr factoextra GGally ggplot2 ggpubr ggrepel gridExtra here kableExtra Matrix optparse plotly pROC readxl tidyverse numpy plotly
Free
210
polyasite_workflow
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Pipeline for the processing of 3' end sequencing libraries
public

public

Pipeline to infer poly(A) site clusters through processing of 3' end sequencing libraries prepared according to various proto...
bigWig bedGraphToBigWig BEDTools Cutadapt SAMtools Snakemake
Free
72
asm-to-reference-alignment
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Reference alignment workflow
public

public

configfile=config/config.yaml threads=200 snakemake --configfile $configfile --cores $threads --use-conda -p Or if you want t...
bigWig csvtk rustybam BCFtools bedGraphToBigWig BEDTools GenomicRanges GLUE karyoploteR Minimap2 Pandas SAMtools seqtk Snakemake argparse cowplot data.table ggnewscale ggplot2 ggrepel RColorBrewer scales tidyverse
Free
52
mu-chip
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muChip Analysis Workflow: Trackhub Creation and Sample Visualization
public

public

Snakemake workflow to analyze muChip experiments. Creates a trackhub with called peaks and domains as well as fragment pileup...
bigWig macs2 trackhub ucsc-bedclip bedGraphToBigWig BEDTools FastQC Picard SAMtools Snakemake Trimmomatic trackhub morphology analysis
Free
57
coop-tf-chipseq
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ChIP-seq analysis pipeline used in Bragdon et. al. 2022.
public

public

Snakemake workflow used to analyze ChIP-seq data for the 2022 publication Cooperative assembly confers regulatory spec...
bigWig MACS2 BEDTools DESeq2 FastQC Pandas SAMtools Snakemake argparse forcats GGally ggplot2 ggrepel ggthemes gridExtra gtable magrittr psych seriation tidyverse viridis numpy scipy
Free
50
biseps_workflow
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Snakemake workflow: biseps
public

public

This is a snakemake pipeline for bisulfite sequencing data, it implements: Adapter trimming and quality check Qua...
bigWig bedGraphToBigWig DeepTools FastQC MultiQC Pandas SAMtools seqtk Snakemake Trimmomatic Bismark numpy Sequence analysis
Free
22
ssds
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Single-stranded DNA Sequencing (SSDS) nf-core pipeline
public

public

nf-core/ssds is a bioinformatics best-practice analysis pipeline for Single-Stranded DNA Sequencing (SSDS) pipeline. The p...
bigWig bedGraphToBigWig BEDTools BWA DeepTools FastQC MultiQC Nextflow Picard SAMtools Trim_Galore SSDS
Free
21
mnaseseq
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MNase-seq analysis pipeline using BWA and DANPOS2.
public

public

nfcore/mnaseseq is a bioinformatics analysis pipeline used for DNA sequencing data obtained via micrococcal nuclease diges...
bigWig preseq BamTools bedGraphToBigWig BEDTools BWA Cutadapt DeepTools FastQC GFFutils MultiQC Picard SAMtools Trim_Galore wigToBigWig Sequence analysis
Free
34
chipseq
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ChIP-seq peak-calling, QC and differential analysis pipeline.
public

public

nfcore/chipseq is a bioinformatics analysis pipeline used for Chromatin ImmunopreciPitation sequencing (ChIP-seq) data. On...
bigWig chromap macs2 preseq BamTools bedGraphToBigWig BEDTools Bowtie 2 BWA Consensus DeepTools DESeq2 FastQC FeatureCounts gffread GFFutils homer khmer MultiQC Nextflow Picard SAMtools STAR Trim_Galore Immunoprecipitation experiment
Free
65
atacseq
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ATAC-seq peak-calling, QC and differential analysis pipeline
public

public

nfcore/atacseq is a bioinformatics analysis pipeline used for ATAC-seq data. The pipeline is built using Nextflow , a ...
bigWig chromap macs2 preseq umi_tools ataqv BamTools bedGraphToBigWig BEDTools Bowtie 2 BWA DeepTools DESeq2 FastQC FeatureCounts gffread GFFutils homer khmer MultiQC Nextflow Picard SAMtools STAR Trim_Galore ATAC-seq
Free
70
cutandrun
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Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
public

public

nf-core/cutandrun is a best-practice bioinformatic analysis pipeline for CUT&RUN, CUT&Tag, and TIPseq experimental protoco...
bigWig macs2 preseq tabix ucsc-bedclip PCAtools bedGraphToBigWig BEDTools Bowtie 2 DeepTools FastQC GFFutils MultiQC Nextflow Picard SAMtools PyYAML Trim_Galore Protein interaction experiment
Free
78