Introduction

nf-core is by design a collaborative effort, and would not exist if it were not for the efforts of many dedicated contributors.

Contributors

The nf-core pipelines and community is driven by many individuals, listed below. This list updates automatically.

Want to see who's working on what? See the contributor leaderboard on the Statistics page.

Github user LaurenceKuhl Github user heuermh Github user adamrtalbot Github user hrydbeck Github user praveenraj2018 Github user lescai Github user MCMandR Github user Aratz Github user alexthiery1 Github user johnne Github user Gwennid Github user CharlotteAnne Github user kstawiski Github user christopher-mohr Github user lokeshbio Github user scwatts Github user ewels Github user kviljoen Github user lassefolkersen Github user charles-plessy Github user kevbrick Github user chuan-wang Github user macroscian Github user pditommaso Github user drewjbeh Github user MartaSanvicente Github user lconde-ucl Github user sc13-bioinf Github user jonasscheid Github user jspaezp Github user subwaystation Github user RaqManzano Github user m3hdad Github user sk-sahu Github user dkoppstein Github user kodayu Github user veeravalli Github user matq007 Github user SusiJo Github user jeantristanb Github user davidmasp Github user sandrocarollo Github user rsuchecki Github user shinthor Github user FelixKrueger Github user chris-cheshire Github user jtangrot Github user xlinxlin Github user mvanins Github user mdeboth Github user nvk747 Github user christopher-hakkaart Github user ltosti-tagomics Github user tfalkarkea Github user amayer21 Github user kbestak Github user Ghepardo Github user lwratten Github user senthil10 Github user Precancer Github user ryanyord Github user Leon-Bichmann Github user davidecarlson Github user MillironX Github user alyssa-ab Github user sminot Github user jordeu Github user arontommi Github user fhausmann Github user axelwalter Github user raysloks Github user orionzhou Github user charlotte-west Github user RHReynolds Github user drpowell Github user carpanz Github user sguizard Github user emnilsson Github user FloWuenne Github user jmuhlich Github user alxndrdiaz Github user ppericard Github user jfnavarro Github user G-Sarah Github user AntoniaSchuster Github user dladd Github user tamara-hodgetts Github user Mxrcon Github user muffato Github user sdomanskyi Github user TCLamnidis Github user evanfloden Github user remiolsen Github user c-mertes Github user alexandregilardet Github user DiegoBrambilla Github user silviamorins Github user KarishmaVal Github user lbeltrame Github user fmalmeida Github user cying111 Github user mjamy Github user thanhleviet Github user GCJMackenzie Github user mjsteinbaugh Github user wbau Github user nictru Github user nh13 Github user caspargross Github user AndreaGuarracino Github user brucemoran Github user Caroline-99 Github user lathikaa Github user snafees Github user ljmesi Github user edmundmiller Github user DSchreyer Github user jzohren Github user bj-w Github user higsch Github user Vivian-chen16 Github user MiguelJulia Github user alessiovignoli Github user Keerthana-Bhaskaran-TG Github user robomics Github user venkan Github user cmgg-be Github user stevekm Github user chadisaad Github user Felix-Kummer Github user yxian9 Github user daichengxin Github user sven1103 Github user fabianegli Github user avantonder Github user ashildv Github user CKComputomics Github user Zethson Github user mattheww95 Github user plarosa Github user heylf Github user sam-white04 Github user JohannesKersting Github user scarlhoff Github user Rotholandus Github user teemuronkko Github user johandahlberg Github user bioinformatist Github user PayamEmami Github user ryanjameskennedy Github user lmtani Github user jun-wan Github user aanil Github user saramonzon Github user noirot Github user WangHong007 Github user margotl9 Github user amchakra Github user dariader Github user vladsavelyev Github user alesssia Github user medulka Github user mglubber Github user na399 Github user berguner Github user jahdoos Github user jemten Github user cmatKhan Github user glormph Github user reganhayward Github user Khajidu Github user alexhbnr Github user fa2k Github user atrigila Github user erikrikarddaniel Github user jfy133 Github user sima-r Github user projectoriented Github user azedinez Github user MariekeVromman Github user vezzi Github user priesgo Github user aidaanva Github user amizeranschi Github user mirpedrol Github user ErikDanielsson Github user sofiahag Github user lbarquist Github user paulklemm Github user ZandraFagernas Github user klkeys Github user noecochetel Github user sirselim Github user adamjtaylor Github user marinawitherell Github user smoe Github user mahesh-panchal Github user rannick Github user bjlang Github user egonw Github user kafkasl Github user sdjebali Github user luisas Github user phoenixAja Github user ssnn-airr Github user colindaven Github user firuegas Github user JackCurragh Github user nvnieuwk Github user jlorent Github user ZWael Github user fevac Github user bewt85 Github user grst Github user cavenel Github user alaindomissy Github user Joon-Klaps Github user KevinMenden Github user maxulysse Github user Midnighter Github user Hammarn Github user pranathivemuri Github user ErikaKvalem Github user grunwald Github user szilvajuhos Github user lucacozzuto Github user fu Github user angelovangel Github user alexthiery Github user svarona Github user PeterBailey Github user husensofteng Github user WackerO Github user drejom Github user TomKellyGenetics Github user nickhsmith Github user likelet Github user wassimsalam01 Github user allaway Github user Gabriel-A-Barrett Github user mribeirodantas Github user leipzig Github user rhr-cosyne Github user nservant Github user luiskuhn Github user daisymut Github user zachary-foster Github user yuukiiwa Github user ojziff Github user evasterviga Github user combiz Github user marcel-keller Github user danclaytondev Github user suhrig Github user matrulda Github user scorreard Github user gregorysprenger Github user hmehlan Github user steffenlem Github user ameynert Github user ctuni Github user MatthiasZepper Github user abhi18av Github user george-hall-ucl Github user tillenglert Github user LouisLeNezet Github user marissaDubbelaar Github user adomingues Github user FriederikeHanssen Github user sateeshperi Github user rhagenson Github user jannikseidelQBiC Github user Darcy220606 Github user abartlett004 Github user jordwil Github user jenmuell Github user ramprasadn Github user jasmezz Github user ejseqera Github user asp8200 Github user sysbiocoder Github user Daniel-VM Github user winni2k Github user d4straub Github user jcurado-flomics Github user pinin4fjords Github user robsyme Github user a4000 Github user LilyAnderssonLee Github user peterpru Github user lucidif Github user louperelo Github user malinlarsson Github user vjmarteau Github user adf-ncgr Github user cjfields Github user jianhong Github user prototaxites Github user SpikyClip Github user bozmik Github user zxl124 Github user Eletham Github user hkaspersen Github user willros Github user rafalstepien Github user apeltzer Github user jburos Github user tjcreedy Github user chelauk Github user olgabot Github user gdevailly Github user brentp Github user jinmingda Github user Akazhiel Github user jpfeuffer Github user bensouthgate Github user sirclockalot Github user alneberg Github user maxibor Github user marchoeppner Github user fasterius Github user bounlu Github user lkuchenb Github user BarryDigby Github user asafpr Github user ypriverol Github user TrisKast Github user mariach Github user mashehu Github user phanhung2 Github user csawye01 Github user rfenouil Github user lpantano Github user CarsonJM Github user sofstam Github user ignaciot Github user kubranarci Github user stan0610 Github user daisyhan97 Github user danilodileo Github user ktrns Github user JoseEspinosa Github user Galithil Github user fbdtemme Github user athbaltzis Github user msanvicente Github user antunderwood Github user adrlar Github user pcantalupo Github user drpatelh Github user SPPearce Github user phue Github user IdoBar Github user vsmalladi Github user asmaali98 Github user HadrienG Github user ggabernet Github user tiagochst Github user rivera10 Github user Lehmann-Fabian Github user ATpoint Github user t-neumann Github user lcabus-flomics Github user sruthipsuresh Github user PhilPalmer Github user Lucpen Github user tavareshugo Github user ekushele Github user MagdalenaZZ Github user matthdsm Github user grantn5 Github user njspix Github user nithyaj12 Github user KochTobi Github user MatthewJM96 Github user glichtenstein Github user skrakau Github user jma1991 Github user valentinoruggieri Github user tomsing1 Github user pprieto Github user tbugfinder Github user rjpbonnal

Organisations

Some of the organisations running nf-core pipelines are listed below, along with a key person who you can contact for advice.

Note
Is your group missing? Please submit a pull request to add yourself! It's just a few lines in a simple YAML file.
The NGI provides next-generation sequencing services for Swedish academic groups. Many of the nf-core pipelines started life as SciLifeLab / NGI workflows.
The Quantitative Biology Center provides a one-stop-shop for access to high-throughput technologies in the life sciences and the required bioinformatics analysis. As a bioinformatics core facility, we provide advanced data analysis techniques.
The Francis Crick Institute is an organisation dedicated to understanding the fundamental biology underlying health and disease.
Improving the health and quality of life of humans and animals is the goal of the research-driven pharmaceutical company Boehringer Ingelheim. The focus in doing so is on diseases for which no satisfactory treatment option exists to date. The company therefore concentrates on developing innovative therapies that can extend patients’ lives. In animal health, Boehringer Ingelheim stands for advanced prevention.
Seqera is simplfying data analysis pipelines across cluster and cloud. As the maintainers of the Nextflow project we focus on enabling high-throughput computing solutions that streamline complex pipelines.
The Centre for Genomic Regulation (CRG) is an international biomedical research institute of excellence, based in Barcelona, Spain, whose mission is to discover and advance knowledge for the benefit of society and public health.
The Genome Institute of Singapore (GIS) is a national initiative for Singapore with a global vision that seeks to use genomic sciences to achieve extraordinary improvements in human health and public prosperity.
The Competence Centre for Genome Analysis Kiel is funded by the German Research Foundation and specialises in high-throughput sequencing of genomes.
The Wellcome Sanger Institute is one of the premier centres of genomic discovery and understanding in the world. It leads ambitious collaborations across the globe to provide the foundations for further research and transformative healthcare innovations.
The Beatson Institute is one of Cancer Research UK’s core-funded institutes. They have built an excellent reputation for basic cancer research, including world-class metabolism studies and renowned in vivo modelling of tumour growth and metastasis.
The Swedish University of Agricultural Sciences is an international organisation providing top class research, education and environmental analysis in the sciences for sustainable life.
The International Agency for Research on Cancer is the specialized cancer agency of the World Health Organization. The objective of the IARC is to promote international collaboration in cancer research.
Lifebit is a London-based biotech start-up which offers an intelligent genomics platform to researchers and their corresponding organisations for scalable, modular and reproducible genomic analysis.
Sun Yat-sen University Cancer Center is a comprehensive cancer centre which provides clinical care to patients, education (students & CME), perform research and prevention activities.
The BioFrontiers Institute at the University of Colorado (CU) is an interdisciplinary hub for bioscience research and education with a focus on improving human health.
The Gregor Mendel Institute of Molecular Plant Biology, an Institute of the Austrian Academy of Sciences, is dedicated to basic research in diverse aspects of plant molecular biology.
The Research Institute of Molecular Pathology (IMP) is a basic research institute in molecular biology, based at the Vienna Biocenter in Austria.
City of Hope is a private, not-for-profit clinical research center, hospital and graduate medical school located in Duarte, California, United States.
IISER Mohali is an autonomous academic and research institution at Mohali, Punjab, India.
The DZNE investigates the causes of neurodegenerative diseases and develops novel strategies for prevention, treatment and care.
Founded in 1831, New York University is now one of the largest private universities in the United States. Of the more than 3,000 colleges and universities in America, New York University is one of only 60 member institutions of the distinguished Association of American Universities.
Royal Botanic Gardens Victoria is one of the world's leading botanic gardens and a centre of excellence for horticulture, science and education.
NBIS is a distributed national bioinformatics infrastructure, supporting life sciences in Sweden.
The Institut Curie is a private nonprofit organization created in 1909 which combines a leading European cancer research center with a hospital group. The Institut Curie Bioinformatics platform is composed of biostatisticians and software engineers who offer a multidisciplinary expertise to support the biotechnological platforms, the research units and the hospital in their daily activities.
CZ Biohub is an independent, non-profit medical research organization working in collaboration with UC San Francisco, Stanford University and UC Berkeley. Our vision is to develop and apply technologies that will enable doctors to cure, prevent or manage all diseases during our children’s lifetime.
The institute is focused on studying all aspects of learning and memory; specifically, it has received over US$50 million to study Alzheimer's, schizophrenia and similar diseases.
Our mission in the RISE Lab at Unversity of California is to develop technologies that enable applications to interact intelligently and securely with their environment in real time.
The Institut Pasteur is a private, non-profit foundation. Its mission is to help prevent and treat diseases, mainly those of infectious origin, through research, teaching, and public health initiatives.
To build on the track record set by India in general and Bangalore in particular, to enable India to play a key role in the global IT scenario through a world class institute with a focus on education and research, entrepreneurship and innovation.
The Max Planck Institute of Biochemistry aims to understand the structure and function of proteins - from single molecules to complex organisms.
The research that is carried out at the Linnaeus University Centre for Ecology and Evolution in Microbial model Systems (EEMiS) is focused on marine environments in the Baltic Sea – on the border between sea and land, in coastal waters and in the open sea.
Baylor College of Medicine is a health sciences university that creates knowledge and applies science and discoveries to further education, healthcare and community service locally and globally.
The MethylGrammar Lab at the Hebrew University School of Medicine is developing tools for analyzing bisulfite sequencing and other epigenomic sequencing methods. We are interested in epigenomic biomarkers of disease, especially DNA methylation.
The National Institute for Biological Standards and Control (NIBSC) plays a leading national and international role in assuring the quality of biological medicines and diagnostics.
Ardigen enables AI transformation for biotech and pharmaceutical companies to leverage the full potential of data. The company delivers value at the intersection of biology and computational methods to increase the likelihood of success and accelerate the drug discovery process. With our platforms based on advanced algorithms and state-of-the-art technology, we help researchers to get scientific insights from a large amount of data, leading to new discoveries and breakthroughs in fields such as personalized medicine and drug development.
The UCL Cancer Institute is the hub for cancer research at University College London, one of the World's leading universities. The Institute draws together over 400 talented scientists who are working together to translate research discoveries into developing kinder, more effective therapies for cancer patients.
Flomics Biotech is developing cell-free RNA liquid biopsies for early detection of complex diseases. We combine optimized molecular biology protocols with machine learning algorithms to obtain accurate, reproducible and meaningful results that can be easily implemented in the clinical practice.
The MRC Human Genetics Unit discovers how changes in our DNA impact our lives. We combine the latest computational and experimental technologies to investigate how our genomes work to control the function of molecules, cells and tissues in people and populations.
The DRESDEN-concept Genome Center is a German competence center for next generation sequencing. We offer services for data generation and bioinformatics in the areas of single cell applications, various short read sequencing applications, and long read genome sequencing and assembly.
Bioinformatics Laboratory at the University of Tsukuba works on the development of bioinformatic methods and software and deployment of bioinformatics and collaborative research. We also offer the training of 'bioinfo-native', who can develop new bioinformatic methods.
RIKEN is Japan's largest comprehensive research institution renowned for high-quality research in a diverse range of scientific disciplines. Researchers at the Center for Biosystems Dynamics Research (BDR) strive to elucidate the biological functions that unfold within the body during an organism’s lifespan, by grasping lifecycle progression from birth to death as a dynamic process involving the establishment.
The Helmholtz Institute for RNA-based Infection Research combines interdisciplinary expertise with cutting-edge research infrastructure to exploit the vast potential of RNA as a diagnostic, target, and drug to combat infectious diseases.
Whitehead Institute is a non-profit research institution located in Cambridge, MA. The Institute is dedicated to basic biomedical research in order to improve human health.
The University of Liverpool is a public university and a member of the Russell Group of research-led universities. Established as University College Liverpool in 1881, it opened its doors to its first set of students in 1882. The university’s motto translates into English as ‘These days of peace foster learning’.
Institute of Zoology (IOZ), Chinese Academy of Sciences (CAS), is a government-funded research institution in zoological sciences. It has a long history of over 80 years. The predecessor of IOZ was Fan Memorial Institute of Biology founded in 1928.
The University of Pavia is one of the world’s oldest academic institutions, with its foundations existing as early as the 9th Century. The Department of Biology and Biotechnology “Lazzaro Spallanzani” was created in 2012 with the aim to bring together scientists from 5 different former Departments, whose expertise encompasses fundamental area of life science including Biochemistry, Cytology, Genetics, Microbiology, Molecular Biology, Pharmacology, Physiology, and Zoology. More than 100 people are working at DBB to give raise and support an intensive scientific and academic activity.
The Molecular Geobiology Lab at LMU uses comparative genomics to study the present and past interactions between Earth and biosphere, the evolution of primarily marine organisms and their symbionts, as well as the evolution of biomineralization.
The University of Texas at Dallas (UTD or UT Dallas) is a public university with its main campus in Richardson, Texas. It is the largest public university in the Dallas area and the northernmost campus of the University of Texas system.
Leiden University is a public research university in Leiden, Netherlands. Founded in 1575 by William, Prince of Orange as a reward to the city of Leiden for its defense against Spanish attacks during the Eighty Years' War.
The Policlinico Gemelli is placed at the heart of the health system, by developing and spreading a national and international reference model regarding the management, organization, technology and humanization of the medical field.
The Center for Medical Genetics Ghent has three main objectives: medical services, research and education. We provide our expertise for the diagnosis and care of patients with hereditary diseases. We strive for a better understanding of these hereditary diseases and translate this knowledge in education in a variety of disciplines.
The HKI is an internationally leading centre for the research of new natural products of microbial origin and for the infection biology of pathogenic fungi. Researchers at the HKI investigate the biosynthesis and function of microbial natural products as mediators of biological communication. The focus here is on new active substances to combat infectious diseases and overcome resistance by developing new anti-infective strategies.
The Max Planck Institute for Evolutionary Anthropology unites scientists with various backgrounds (natural sciences and humanities) whose aim is to investigate the history of humankind from an interdisciplinary perspective with the help of comparative analyses of genes, cultures, cognitive abilities, languages and social systems of past and present human populations as well as those of primates closely related to human beings.
The CRUK Manchester Institute is a leading cancer research institute within The University of Manchester, spanning the whole spectrum of cancer research - from investigating the molecular and cellular basis of cancer, to translational research and the development of therapeutics.
The IGDR is deeply engaged in conceiving innovative and multidisciplinary approaches towards a quantitative and dynamic understanding of life. Its research revolves around 3 main scientific themes involving several scientific questions from basic to translational research: From molecule to cell: structure versus dynamics; From cell to organism : an identity case; From genes to cancer and genetic diseases.
As a nation-wide federated consortium, GHGA is building a secure omics data infrastructure that provides a framework for the use of human genome data for research purposes while preventing data misuse. Providing standardised, comparable, and reproducible omics workflows for the research community is one goal of GHGA, whereby we align with the nf-core community to curate best-practise workflows.
Element Biosciences is a multi-disciplinary startup focused on innovating genetic analysis tools for the research and diagnostic markets. Element Biosciences' mission is to empower the scientific community with more freedom and flexibility to accelerate our collective impact on humanity.
The Institut Pasteur Dakar Foundation (IPD) is a non-profit association of public utility, concerned with promoting public health and well-being in West Africa.
Healx is an AI-powered, patient-inspired tech company, accelerating the discovery and development of treatments for rare diseases.
Human Technopole is Italy’s life science institute, located at the heart of MIND (Milano Innovation District). Human Technopole’s overarching mission is to improve human health and well-being, by: carrying out frontier research in the life sciences aimed at developing novel approaches in preventive and personalised medicine; setting up and operating scientific services and facilities, to also be made available to external researchers; training the next generation of leading scientists; promoting innovation and progress through technology transfer. Once fully operational, HT will employ over 1.000 scientists from all over the world.
The Hartree Centre helps UK businesses and organisations of any size to explore and adopt supercomputing, data science and artificial intelligence (AI) technologies for enhanced productivity, smarter innovation and economic growth. Backed by significant UK government funding and strategic partnerships with industry leaders such as IBM, Atos and the University of Liverpool, the Hartree Centre is home to some of the most advanced digital technologies and experts in the UK.
Sydney Informatics Hub is a core research facility at the University of Sydney. We work towards enabling excellence in data and compute intensive research. We provide support, training, and expertise in statistics, data science, artificial intelligence, bioinformatics, software engineering, simulation, visualisation, and research computing.
As tuberculosis research in South Africa has become increasingly reliant on molecular biotechnologies, the volume of data produced has grown considerably. The South African Tuberculosis Bioinformatics Initiative (SATBBI) was created in response to this growth, creating a group of bioinformatics researchers engaged with the tuberculosis research community in South Africa.
University of Magallanes if a public chilean university, located in the Magallanes region.
The Rega Institute for Medical Research is a Belgian scientific establishment that is part of the Catholic University of Leuven (Leuven) in central Belgium. The Rega Institute is an interfacultary biomedical research institute consists of departments of medicine and pharmacology.

Projects we are involved with

A number of large projects are committing to working with the nf-core community for data analysis pipelines. You can see an overview of these below.

German National Sequencing Initiative

The German Funding Body (DFG) has approved funding to establish 4 national high-throughput sequencing centers in Germany. The project will rely on nf-core pipelines for analyzing large-scale genomics data. Contributors from the Kiel, Tübingen and Dresden sites are already actively contributing to nf-core, and the other sequencing center in Cologne/Bonn (West German Genome Center) has committed to joining and contributing its expertise.

EASI-Genomics

EASI-Genomics provides easy and seamless access to cutting-edge DNA sequencing technologies to researchers from academia and industry, within a framework that ensures compliance with ethical and legal requirements, as well as FAIR and secure data management. EASI-Genomics aims to build a community of practice, which leverages advanced sequencing technologies beyond country and sector borders to tackle global challenges in science. It organizes competitive calls to get fully-funded access to state-of-the-art facilities and services, including integrative data analysis.

EASI-Genomics partners are committed to working within community best-practices for the bioinformatics processing of the data that they produce. To this end they will use nf-core pipelines to process data and contribute new developments and pipelines within the nf-core framework.

BovReg

BovReg is a H2020 project to form a consortium that will provide a comprehensive map of functionally active genomic features in cattle and how their (epi)genetic variation in beef and dairy breeds translates into phenotypes.

BovReg reference bioinformatics pipelines will adhere to nf-core guidelines in order to deliver reproducible data analyses to the community.

Dockstore

Dockstore is a platform used by researchers across the world to share reproducible computational analyses and hosts hundreds of individual tools and workflows created by more than a hundred different contributors.

By using lightweight containerization technology along with the essential metadata needed for combining tools into scientific analysis "recipes", Dockstore allows users to create, share, publish (using citable DOIs) and reproducibly reuse these recipes across platforms and compute environments.

Workflow Hub

Workflow Hub was created as part of the EOSC-Life WP2: Tools Collaboratory and Research Objects to glue in federated workflow and tool descriptions across research infrastructures.

It is workflow system agnostic, supports a repository of workflows in native and standardised form and the virtual aggregation of established tool, workflow and registries to support discovery over a fragmented ecosystem. The federated registry will support a common API to simplify access for tool developers.