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125 Workflows visible to you, out of a total of 184

A simple bacterial assembly and annotation pipeline

Introduction

Short Read Assembly

This pipeline is primarily for bacterial assembly of next-generation sequencing reads. It can be used to quality trim your reads using Skewer and performs basic sequencing QC using FastQC. Afterwards, the pipeline performs read assembly using Unicycler. Contamination of the assembly is checked using Kraken2 to verify sample purity.

Long Read Assembly

For users that only have Nanopore data, the pipeline quality ...

Type: Nextflow

Creator: Andreas Wilm, Alexander Peltzer

Submitter: Finn Bacall

nf-core/bactmap

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

Introduction

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 / singularity containers making installation trivial and results highly reproducible.

Documentation

The nf-core/bactmap pipeline comes with documentation about the pipeline, found in the docs/ directory:

Installation Pipeline ...

Type: Nextflow

Creator: Anthony Underwood

Submitter: Finn Bacall

Introduction

The nf-core/bcellmagic pipeline is built to analyze B-cell repertoire sequencing data. It makes use of the Immcantation 2.5.0 toolset and requires targeted sequencing data of the V, D, J and C regions of the B-cell receptor (primers for the V and C genes).

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 / singularity containers making installation trivial and results highly ...

Type: Nextflow

Creator: Gisela Gabernet, Simon Heumos, Alexander Peltzer

Submitter: Finn Bacall

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

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