nf-core/vipr is a bioinformatics best-practice analysis pipeline for assembly and intrahost / low-frequency variant calling for viral samples. 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. Pipeline Steps

Step Main program/s

Trimming, combining of read-pairs per sample and QC Skewer, FastQC

Decontamination ...

nfcore/viralrecon is a bioinformatics analysis pipeline used to perform assembly and intrahost/low-frequency variant calling for viral samples. The pipeline currently supports metagenomics and amplicon sequencing data derived from the Illumina sequencing platform. This pipeline is a re-implementation of the SARS_Cov2_consensus-nf and SARS_Cov2_assembly-nf pipelines initially developed by Sarai Varona and Sara Monzon from BU-ISCIII. Porting both of these pipelines to nf-core was an international ...

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 ...

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. ...

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/ ...

nf-kmer-similarity

This is a Nextflow workflow for running k-mer similarity

Usage

With a samples.csv file:

nextflow run czbiohub/nf-kmer-similarity --outdir s3://olgabot-maca/nf-kmer-similarity/ --samples samples.csv

With R1, R2 read pairs:

nextflow run czbiohub/nf-kmer-similarity --outdir s3://olgabot-maca/nf-kmer-similarity/ \ --read_pairs 's3://olgabot-maca/sra/homo_sapiens/smartseq2_quartzseq/{R1,R2}.fastq.gz,s3://olgabot-maca/sra/danio_rerio/smart-seq/whole_kidney_marrow_prjna393431/*{1,2}.fastq.gz' ...

Precision HLA typing from next-generation sequencing data using OptiType.

Table of Contents

Introduction Quick Start

With Docker With Singularity

Documentation Pipeline DAG

Input fastq Input bam

Credits

Introduction

OptiType is a HLA genotyping algorithm based on integer linear programming. Reads of whole exome/genome/transcriptome sequencing data are mapped against a reference of known MHC class I alleles. To produce accurate 4-digit HLA genotyping predictions, all major and minor HLA-I loci are ...

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 ...

A fully reproducible ancient and modern DNA pipeline in Nextflow and with cloud support..

Introduction

nf-core/eager is a bioinformatics best-practice analysis pipeline for NGS sequencing based ancient DNA (aDNA) data analysis.

The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FASTQ inputs, aligns the reads and performs extensive general NGS and aDNA specific quality-control on the results. It comes with docker, singularity or conda containers making ...

Automated quantitative analysis of DIA proteomics mass spectrometry measurements.

Introduction

nfcore/diaproteomics is a bioinformatics analysis pipeline used for quantitative processing of data independant (DIA) proteomics data.

The workflow is based on the OpenSwathWorkflow for SWATH-MS proteomic data. DIA RAW files (mzML) serve as inputs and library search is performed based on a given input spectral library. If specified internal retention time standarts (irts) will be used to align library ...

Hybrid genome assembly.

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 containers making installation trivial and results highly reproducible.

Documentation

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

Installation Pipeline configuration

Local installation Adding your own system config Reference genomes

Running the ...

nf-core/deepvariant

Deep Variant as a Nextflow pipeline

A Nextflow pipeline for running the Google DeepVariant variant caller.

What is DeepVariant and why in Nextflow?

The Google Brain Team in December 2017 released a Variant Caller based on DeepLearning: DeepVariant.

In practice, DeepVariant first builds images based on the BAM file, then it uses a DeepLearning image recognition approach to obtain the variants and eventually it converts the output of the prediction in the standard VCF format. ...

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 ...

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/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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

Introduction

nfcore/atacseq is a bioinformatics analysis pipeline used for ATAC-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 libraries of the same sample (picard) ...

Introduction

nfcore/ampliseq is a bioinformatics analysis pipeline used for 16S rRNA amplicon sequencing data.

The workflow processes raw data from FastQ inputs (FastQC), trims primer sequences from the reads (Cutadapt), imports data into QIIME2, generates amplicon sequencing variants (ASV, DADA2), classifies features against the SILVA v132 database, excludes unwanted taxa, produces absolute and relative feature/taxa count tables and plots, plots alpha rarefaction curves, computes alpha and beta ...