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nf-core/cageseq

CAGE-seq pipeline.

Introduction

UNDER DEVELOPMENT

This pipeline is currenlty under development. The workflow is not yet finished.

nf-core/cageseq is a pipeline built for the analysis of CAGE-sequencing data.

Analysis steps consist of adapter and artefact trimming (cuatadapt), alignment to a reference (STAR) and CAGE tag counting. Additionally, several quality control steps (FastQC, MultiQC) are included to allow for easy verification of results after a run.

The pipeline is built ...

Type: Nextflow

Creator: Kevin Menden

Submitter: Finn Bacall

Introduction

nfcore/chipseq is a bioinformatics analysis pipeline used for Chromatin ImmunopreciPitation sequencing (ChIP-seq) data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Pipeline summary

Raw read QC (FastQC) Adapter trimming (Trim Galore!) Alignment (BWA) Mark duplicates (picard) Merge alignments from multiple ...

Type: Nextflow

Creator: Philip Ewels

Submitter: Finn Bacall

Identifies non-coding RNAs using Rfams covariance models

Type: Common Workflow Language

Creator: Arnaud Meng, Maxim Scheremetjew

Submitter: Finn Bacall

Chunked version of phmmer-v3.2.cwl

Type: Common Workflow Language

Creator: Maxim Scheremetjew

Submitter: Finn Bacall

Transcriptome assembly workflow (paired-end version)

Type: Common Workflow Language

Creator: Arnaud Meng, Maxim Scheremetjew

Submitter: Finn Bacall

Transcriptome assembly workflow (single-end version)

Type: Common Workflow Language

Creator: Arnaud Meng, Maxim Scheremetjew

Submitter: Finn Bacall

Transcripts annotation workflow

Type: Common Workflow Language

Creator: Arnaud Meng, Maxim Scheremetjew, Michael Crusoe

Submitter: Finn Bacall

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