AliNe — Peer-reviewed • Rank 4.1 • Science 98%

AliNe: A Flexible and Efficient Nextflow Pipeline for Read Alignment - Published in JOSS (2025)

nf-gwas-pipeline — Peer-reviewed • Rank 4.7 • Science 95%

nf-gwas-pipeline: A Nextflow Genome-Wide Association Study Pipeline - Published in JOSS (2021)

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis — Peer-reviewed • Rank 3.6 • Science 93%

ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - Published in JOSS (2022)

io.nextflow:nextflow • Rank 17.5 • Science 77%

A DSL for data-driven computational pipelines

nf-core • Rank 22.0 • Science 67%

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

dockstore • Rank 10.3 • Science 77%

An app store for scientific workflows, tools, notebooks, and services

scrnaseq • Rank 9.6 • Science 77%

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

ampliseq • Rank 9.1 • Science 77%

Amplicon sequencing analysis workflow using DADA2 and QIIME2

smrnaseq • Rank 8.5 • Science 77%

A small-RNA sequencing analysis pipeline

chipseq • Rank 8.4 • Science 77%

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

viralrecon • Rank 8.4 • Science 77%

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

cutandrun • Rank 7.5 • Science 77%

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

mhcquant • Rank 7.3 • Science 77%

Identify and quantify MHC eluted peptides from mass spectrometry raw data

clipseq • Rank 6.4 • Science 77%

CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.

bactmap • Rank 6.2 • Science 77%

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

dualrnaseq • Rank 6.0 • Science 77%

Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.

metapep • Rank 5.5 • Science 77%

From metagenomes to epitopes and beyond

rnadnavar • Rank 4.6 • Science 77%

Pipeline for RNA and DNA integrated analysis for somatic mutation detection

isoseq • Rank 4.6 • Science 77%

Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.

sarek • Rank 10.9 • Science 67%

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

mag • Rank 9.5 • Science 67%

Assembly and binning of metagenomes

nanoseq • Rank 8.8 • Science 67%

Nanopore demultiplexing, QC and alignment pipeline

fetchngs • Rank 8.7 • Science 67%

Pipeline to fetch metadata and raw FastQ files from public databases

methylseq • Rank 8.7 • Science 67%

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

bacass • Rank 7.5 • Science 67%

Simple bacterial assembly and annotation pipeline

airrflow • Rank 7.4 • Science 67%

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

funcscan • Rank 7.4 • Science 67%

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

demultiplex • Rank 7.4 • Science 67%

Demultiplexing pipeline for sequencing data

hlatyping • Rank 7.2 • Science 67%

Precision HLA typing from next-generation sequencing data

nascent • Rank 7.2 • Science 67%

Nascent Transcription Processing Pipeline

epitopeprediction • Rank 7.1 • Science 67%

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

pangenome • Rank 6.7 • Science 67%

Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.

pipelines-nextflow • Rank 6.7 • Science 67%

A set of workflows written in Nextflow for Genome Annotation.

crisprseq • Rank 6.3 • Science 67%

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`).

bamtofastq • Rank 6.0 • Science 67%

Converts bam or cram files to fastq format and does quality control.

mcmicro • Rank 5.6 • Science 67%

An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

circdna • Rank 5.4 • Science 67%

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.

imcyto • Rank 5.2 • Science 67%

Image Mass Cytometry analysis pipeline

hgtseq • Rank 5.1 • Science 67%

A pipeline to investigate horizontal gene transfer from NGS data

genomeassembler • Rank 5.0 • Science 67%

Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads

hicar • Rank 4.9 • Science 67%

Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.

mikrokondo • Rank 4.5 • Science 67%

A simple pipeline for bacterial assembly and quality control

coproid • Rank 4.5 • Science 67%

Coprolite host Identification pipeline

marsseq • Rank 4.0 • Science 67%

MARS-seq v2 pre-processing pipeline with velocity

radseq • Rank 2.9 • Science 67%

Variant-calling pipeline for Restriction site-associated DNA sequencing (RADseq).

euryale • Rank 2.7 • Science 67%

A pipeline for taxonomic classification and functional annotation of metagenomic reads. Based on MEDUSA

rangeland • Rank 2.4 • Science 67%

Pipeline for remotely sensed imagery. The pipeline processes satellite imagery alongside auxiliary data in multiple steps to arrive at a set of trend files related to land-cover changes.

nextits • Rank 2.2 • Science 67%

A pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio

cnr-flow • Rank 1.6 • Science 64%

CUT&RUN-Flow, A Nextflow pipeline for QC, tag trimming, normalization, and peak calling for data from CUT&RUN experiments.

rnafusion • Rank 8.4 • Science 57%

RNA-seq analysis pipeline for detection of gene-fusions

taxprofiler • Rank 8.4 • Science 57%

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

differentialabundance • Rank 7.9 • Science 57%

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

hic • Rank 7.4 • Science 57%

Analysis of Chromosome Conformation Capture data (Hi-C)

proteinfold • Rank 7.1 • Science 57%

Protein 3D structure prediction pipeline

configs • Rank 10.0 • Science 54%

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

fastquorum • Rank 4.9 • Science 59%

Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)

rnasplice • Rank 6.9 • Science 57%

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

spatialvi • Rank 6.8 • Science 57%

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

rnavar • Rank 6.2 • Science 57%

gatk4 RNA variant calling pipeline

circrna • Rank 6.1 • Science 57%

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

metatdenovo • Rank 5.8 • Science 57%

Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.

gwas • Rank 5.8 • Science 57%

UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies

kmermaid • Rank 5.7 • Science 57%

k-mer similarity analysis pipeline

test-datasets • Rank 8.1 • Science 54%

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

nanostring • Rank 4.8 • Science 57%

An analysis pipeline for Nanostring nCounter expression data.

molkart • Rank 4.5 • Science 57%

A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)

modules • Rank 12.5 • Science 49%

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

mira-nf • Rank 4.5 • Science 57%

phyloplace • Rank 3.7 • Science 57%

nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.

proteomicslfq • Rank 6.7 • Science 54%

Proteomics label-free quantification (LFQ) analysis pipeline

rnaseq • Rank 11.6 • Science 49%

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

viralintegration • Rank 5.6 • Science 54%

Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.

callingcards • Rank 2.3 • Science 57%

A pipeline for processing calling cards data

bpertussis-ciwgs • Rank 1.1 • Science 57%

Culture-Independent Whole Genome Sequencing (CIWGS) Read Filter Pipeline 🧪🧬🖥️

atacseq • Rank 8.5 • Science 49%

ATAC-seq peak-calling and QC analysis pipeline

variantcatalogue • Rank 2.5 • Science 54%

Pipeline to generate variant catalogues, a list of variants and their frequencies in a population, from whole genome sequences.

raredisease • Rank 8.4 • Science 44%

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

mnaseseq • Rank 4.2 • Science 44%

MNase-seq analysis pipeline using BWA and DANPOS2.

workflows-nextflow • Rank 6.9 • Science 41%

Workflow management with Nextflow and nf-core

website • Rank 10.3 • Science 36%

Code and files for the main nf-core website.

https://github.com/cdcgov/tostadas • Rank 5.2 • Science 36%

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

metaboigniter • Rank 4.5 • Science 31%

Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.

genomeannotator • Rank 3.6 • Science 26%

Pipeline for the identification of (coding) gene structures in draft genomes.

germline-structuralv-nf • Science 57%

Germline structural variant calling pipeline for short read WGS datasets

drugresponseeval • Science 57%

Pipeline for testing drug response prediction models in a statistically and biologically sound way.

genomeassembly • Science 75%

Implementation of ToL genome assembly workflows

denovotranscript • Science 57%

A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq

https://github.com/asadprodhan/blastn • Science 23%

How to automatically download blastn database, run blastn, and extract blastn hit sequences?

https://github.com/asadprodhan/how-to-run-kraken2-on-hpc-using-singularity-container-and-nextflow • Science 13%

An intuitive tutorial on Kraken2 metagenomic analysis

https://github.com/cfsan-biostatistics/nowayout • Science 26%

nowayout is a super-fast automated software pipeline for taxonomic classification of Eukaryotic mitochondrial reads.

pathogensurveillance • Science 67%

Surveillance of pathogens using population genomics and sequencing

nf-resequencing-mem • Science 57%

Nextflow resequencing pipeline with bwa-mem and freebayes

https://github.com/australianbiocommons/nextflow_dsl2_template • Science 13%

Template for creating Nextflow DSL2 pipelines

genealignment • Science 65%

An NF-core pipeline to alignment genesets against a given reference genome.

references • Science 57%

nf-core/references is a bioinformatics pipeline that build references, for multiple use cases

nf-fastq2bam • Science 57%

Nextflow pipeline to convert FASTQ files to BAM for WGS and RNA-seq data

drop • Science 57%

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

stableexpression • Science 57%

Pipeline dedicated to finding the most stable genes among a single or multiple expression dataset(s). It is useful in particular for finding the most suitable RT-qPCR reference genes for a specific species.

treeval • Science 65%

Pipelines for the production of Treeval data

sequencecomposition • Science 65%

Nextflow DSL2 pipeline to extract statistics from a genome about its sequence composition