Workflows

What is a Workflow?
1299 Workflows visible to you, out of a total of 1382
Stable

This workflow supports processing of bulk ACT-Seq data from raw reads to genome-wide accessiblity tracks (bigWig) and ACT-Seq peaks. The main steps include read trimming using trimGalore, alignment with bowtie2, coverage generation using samtools and peak calling with MACS2.

Type: Common Workflow Language

Creator: Kersten Breuer

Submitter: Pavlo Lutsik

Stable

This workflow supports processing of bulk CUT'N'RUN data from raw reads to genome-wide accessiblity tracks (bigWig) and CUT'N'RUN peaks. The main steps include read trimming using trimGalore, alignment with bowtie2, coverage generation using samtools and peak calling with MACS2.

Type: Common Workflow Language

Creator: Kersten Breuer

Submitter: Pavlo Lutsik

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creators: None

Submitter: WorkflowHub Bot

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite with ...

Type: Nextflow

Creator: Christopher Hakkaart

Submitter: WorkflowHub Bot

Stable

This workflow supports primary processing of ChIP-Seq data from raw reads to genome-wide ChIP signal tracks and ChIP peaks. The main steps include read trimming using trimGalore, alignment with bowtie2, coverage generation using samtools and peak calling with MACS2.

Type: Common Workflow Language

Creator: Kersten Breuer

Submitter: Pavlo Lutsik

Stable

This workflow supports processing of bulk ATAC-Seq data from raw reads to genome-wide accessiblity tracks (bigWig) and ATAC peaks. The main steps include read trimming using trimGalore, alignment with bowtie2, coverage generation using samtools and peak calling with MACS2.

Type: Common Workflow Language

Creator: Kersten Breuer

Submitter: Pavlo Lutsik

Stable

GenErode pipeline

Snakemake

GitHub repository for GenErode, a Snakemake workflow for the analysis of whole-genome sequencing data from historical and modern samples to study patterns of genome erosion.

Documentation

The full pipeline documentation can be found on the repository wiki.

Citation

If you've ...

Type: Snakemake

Creators: None

Submitter: Verena Kutschera

GitHub Actions CI Status

GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creator: Clinical Genomics Stockholm

Submitter: WorkflowHub Bot

A bioinformatics best-practice analysis pipeline for reconstructing consensus genomes and to identify intra-host variants from metagenomic sequencing data or enriched based sequencing data like hybrid capture.

Type: Nextflow

Creators: Joon-Klaps , Joon-Klaps

Submitter: WorkflowHub Bot

GitHub Actions CI Status GitHub Actions Linting Status AWS CI [![Cite ...

Type: Nextflow

Creator: Pixelgen Technologies AB

Submitter: WorkflowHub Bot

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