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.

cronology • Science 36%

cronology is an automated workflow for Cronobacter whole genome sequence assembly, subtyping and isolate clustering based on NCBI Pathogen Detection Project for Cronobacter.

https://github.com/agahkarakuzu/bids2nf • Science 26%

Emits nextflow channels from Brain Imaging Data Structure data.

iridanextexample • Science 31%

An example pipeline for running on IRIDA Next

arete • Science 54%

AMR/VF LGT focused bacterial genomics analysis workflow

bacannot • Science 49%

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

pixelator • Science 44%

Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)

https://github.com/clinical-genomics/raredisease • Science 31%

CG's rare disease pipeline in next flow, see the main repo here 👇

what_the_phage • Science 57%

WtP: Phage identification via nextflow and docker or singularity

evexplorer • Science 57%

nf-core/evexplorer is a pipeline for analyzing RNA data from extracellular vesicles, compatible with technologies such as nextflex, comboSeq, and ONT with further support forthcoming. evexplorer handles QC, expressed region detection, library size normalization and Differential RNA Expression (DRE)

variantbenchmarking • Science 57%

Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research

panoramaseq • Science 57%

a pipeline to process sequencing based spatial transccriptomics data from in-situ arrays

nf-core-scgs • Science 67%

Single Cell Genome Sequencing data analysis pipeline

scdownstream • Science 57%

A single cell transcriptomics pipeline for QC, integration and making the data presentable

seqinspector • Science 44%

QC pipeline to inspect your sequences

aradeepopsis • Science 85%

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

omnifluss • Science 44%

Computational workflow for virus genome reconstruction

https://github.com/cidgoh/nf-ncov-voc • Science 49%

A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 or Mpox genomes. Workflow is developed in collaboration with VIRUS-MVP (https://github.com/cidgoh/VIRUS-MVP) which can be used to visualize the mutation profiles and functional annotations.