Workflows

Assembly, binning and annotation of metagenomes.

Introduction

This pipeline is for assembly, binning and annotation of metagenomes. It supports both short and long reads, quality trims the reads and adapters with https://github.com/OpenGene/fastp and https://github.com/rrwick/Porechop and performs basic QC with https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.

The pipeline then:

assigns taxonomy to reads using https://ccb.jhu.edu/software/centrifuge/ and/or https://ccb.jhu.edu/software/kraken2/ ...

Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community..

The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.

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. ...

Identify and quantify peptides from mass spectrometry raw data

Introduction

nfcore/mhcquant is a bioinformatics analysis pipeline used for quantitative processing of data dependant (DDA) peptidomics data.

It was specifically designed to analyse immunopeptidomics data, which deals with the analysis of affinity purified, unspecifically cleaved peptides that have recently been discussed intensively in the context of cancer vaccines.

The workflow is based on the OpenMS C++ framework for computational ...

nf-core/guideseq

Pipeline for GUIDE-Seq data analysis. Find off-target cleavage sites..

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/guideseq pipeline comes with documentation about the pipeline, found in the docs/ directory:

Installation Pipeline configuration

Local ...

nf-core/clinvap

Clinical Variant Annotation Pipeline

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/clinvap pipeline comes with documentation about the pipeline, found in the docs/ directory:

Installation Pipeline configuration

Local installation Adding your own system ...

nf-core/crisprvar

Run CRISPResso on genome editing experiments

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/crisprvar pipeline comes with documentation about the pipeline, found in the docs/ directory:

Installation Pipeline configuration

Local installation Adding ...

nf-core/ddamsproteomics

Quantitative shotgun MS proteomics as done in Lehtio lab

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/ddamsproteomics pipeline comes with documentation about the pipeline, found in the docs/ directory:

Installation Pipeline configuration

Local ...