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Search results for pipeline nextflow

189 search results found

Nextflow ⭐ 2,447

A DSL for data-driven computational pipelines

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Awesome Nextflow ⭐ 448

A curated list of nextflow based pipelines

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Bactopia ⭐ 281

A flexible pipeline for complete analysis of bacterial genomes

Flowcraft ⭐ 234

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦

Python package with helper tools for the nf-core community.

Modules ⭐ 180

Repository to host tool-specific module files for the Nextflow DSL2 community!

Assembly and binning of metagenomes

Atacseq ⭐ 145

ATAC-seq peak-calling and QC analysis pipeline

Chipseq ⭐ 144

ChIP-seq peak-calling, QC and differential analysis pipeline.

Ampliseq ⭐ 141

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Nanoseq ⭐ 122

Nanopore demultiplexing, QC and alignment pipeline

Methylseq ⭐ 121

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

Rnafusion ⭐ 120

RNA-seq analysis pipeline for detection gene-fusions

Scrnaseq ⭐ 119

A single-cell RNAseq pipeline for 10X genomics data

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

Viralrecon ⭐ 101

Assembly and intrahost/low-frequency variant calling for viral samples

Emg Viral Pipeline ⭐ 98

VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

Fetchngs ⭐ 93

Pipeline to fetch metadata and raw FastQ files from public and private databases

Dolphinnext ⭐ 92

A graphical user interface for distributed data processing of high throughput genomics

Multiple-choice microscopy pipeline

GWAS Pipeline for H3Africa

Nextflow Demos ⭐ 88

Example Nextflow pipelines and programming techniques

Bacannot ⭐ 85

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

Ncov2019 Artic Nf ⭐ 85

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformat with a focus on ncov2019

Training ⭐ 82

Nextflow training material

Test Datasets ⭐ 81

Test data to be used for automated testing with the nf-core pipelines

Distiller Nf ⭐ 80

A modular Hi-C mapping pipeline

Taxprofiler ⭐ 78

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Master_of_pores ⭐ 77

Nextflow pipeline for analysis of direct RNA Nanopore reads

Callings Nf ⭐ 76

GATK RNA-Seq Variant Calling in Nextflow

Config files used to define parameters specific to compute environments at different Institutions

Vsn Pipelines ⭐ 65

A repository of pipelines for single-cell data in Nextflow DSL2

Raredisease ⭐ 64

Call and score variants from WGS/WES of rare disease patients.

Smrnaseq ⭐ 63

A small-RNA sequencing analysis pipeline

Analysis of Chromosome Conformation Capture data (Hi-C)

Nanoclust ⭐ 59

NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads

Rnaseq Nf ⭐ 59

A proof of concept of RNAseq pipeline

Metontiime ⭐ 57

A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework

hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis

Nextneopi ⭐ 55

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction

Cutandrun ⭐ 54

Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.

Pytest Workflow ⭐ 52

Configure workflow/pipeline tests using yaml files.

YAMP: Yet Another Metagenomic Pipeline

Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads

Ngi Rnaseq ⭐ 49

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

Funcscan ⭐ 49

(Meta-)genome screening for functional and natural product gene sequences

Nextflowsnippets ⭐ 48

This repository hosts a large collection of Nextflow snippets

Simple bacterial assembly and annotation pipeline

Nextflow.py ⭐ 46

Python wrapper around Nextflow.

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

Tractoflow ⭐ 44

TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity

Pipelines Nextflow ⭐ 41

A set of workflows written in Nextflow for Genome Annotation.

Airrflow ⭐ 40

B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

Needlestack ⭐ 39

Multi-sample somatic variant caller

Deepvariant ⭐ 38

Google's DeepVariant variant caller as a Nextflow pipeline

Grape Nf ⭐ 35

An automated RNA-seq pipeline using Nextflow

List of IARC bioinformatics nextflow pipelines

Hlatyping ⭐ 34

Precision HLA typing from next-generation sequencing data

Differentialabundance ⭐ 34

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

Spatialtranscriptomics ⭐ 34

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

Proteomicslfq ⭐ 32

Proteomics label-free quantification (LFQ) analysis pipeline

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

Rnadeseq ⭐ 31

Differential gene expression analysis and pathway analysis of RNAseq data

Demultiplex ⭐ 31

Demultiplexing pipeline for sequencing data

Mhcquant ⭐ 28

Identify and quantify MHC eluted peptides from mass spectrometry raw data

Epitopeprediction ⭐ 28

A bioinformatics best-practice analysis pipeline for epitope prediction and annotation

Multifish ⭐ 28

EASI-FISH analysis pipeline for spatial transcriptomics

Aradeepopsis ⭐ 28

A versatile, fully open-source pipeline to extract phenotypic measurements from plant images

Pangenome ⭐ 28

Renders a collection of sequences into a pangenome graph.

Proteinfold ⭐ 26

Protein 3D structure prediction pipeline

Long Read Proteogenomics ⭐ 26

A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.

Deepvariant ⭐ 26

Deep Variant as a Nextflow pipeline

Pipeliner ⭐ 25

A flexible Nextflow-based framework for the definition of sequencing data processing pipelines

Geneshot ⭐ 25

A proof of concept RNA-Seq pipeline with Nextflow

gatk4 RNA variant calling pipeline

Ngs Preprocess ⭐ 23

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

Bionextflow ⭐ 22

A collection of modules and sub-workflows for Nextflow

Macse_v2_pipelines ⭐ 21

This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MACSE. These pipelines are mostly bash scripts encapsulated within singularity containers and sometimes combined in nextflow workflows.

Rnaseq Nf ⭐ 20

RNAseq analysis pipeline

Master of Pores 2

Variant_catalogue_pipeline ⭐ 20

Variant catalogue pipeline

Kallisto Nf ⭐ 20

A nextflow implementation of Kallisto & Sleuth RNA-Seq Tools

Nanoflow ⭐ 20

🔬 De novo assembly of nanopore reads using nextflow

SPANDx - Comparative genomics for next-generation haploid sequence data

Porefile ⭐ 19

A Nextflow full-length 16S profiling pipeline for ONT reads

Automatic Packaging and Distribution of Bioinformatics Pipelines

Maliampi ⭐ 19

Maximum Likelihood Amplicon Pipeline

TADA - Targeted Amplicon Diversity Analysis - a DADA2-focused Nextflow workflow for any targeted amplicon region

Companion ⭐ 19

Pipeline for automatic eukaryotic parasite annotation

Rnasplice ⭐ 18

rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.

UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

Gatk4_best_practice ⭐ 18

GATK4 Best Practice Nextflow Pipeline

Cookiecutter ⭐ 18

DEPRECIATED! Please use nf-core/tools instead

Crisprseq ⭐ 17

A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).

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