Do you know of an nf-core publication that we're missing? Please make a pull-request.

The nf-core project

Main publication for the main nf-core paper, describing the community and framework:

The nf-core framework for community-curated bioinformatics pipelines

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen

Nat Biotechnology (2020); doi: 10.1038/s41587-020-0439-x

ReadCube: View full text

Preprint for the main nf-core paper (significantly different from the final Nature Biotech paper):

nf-core: Community curated bioinformatics pipelines

Philip Ewels, Alexander Peltzer, Sven Fillinger, Johannes Alneberg, Harshil Patel, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso, Sven Nahnsen

bioRxiv 610741; doi: 10.1101/610741

Article in Nature describing scientific workflows (including nf-core):

Workflow systems turn raw data into scientific knowledge

Jeffrey M. Perkel

Nature 573, 149-150 (2019); doi: 10.1038/d41586-019-02619-z

Pipeline publications


Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 1; peer review: awaiting peer review].

Maxime Garcia, Szilveszter Juhos, Malin Larsson, Pall I. Olason, Marcel Martin, Jesper Eisfeldt, Sebastian DiLorenzo, Johanna Sandgren, Teresita Díaz De Ståhl, Philip Ewels, Valtteri Wirta, Monica Nistér, Max Käller, Björn Nystedt

F1000Research, 9:63 (2020) doi: 10.12688/f1000research.16665.1


CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content

Maxime Borry, Bryan Cordova, Angela Perri, Marsha C. Wibowo, Tanvi Honap, Wing Tung Jada Ko, Jie Yu, Kate Britton, Linus Girdland Flink, Robert C. Power, Ingelise Stuijts, Domingo Salazar Garcia, Courtney A. Hofman, Richard W. Hagan, Thérèse Samdapawindé Kagone, Nicolas Meda, Hélène Carabin, David Jacobson, Karl Reinhard, Cecil M. Lewis Jr., Aleksandar Kostic, Choongwon Jeong, Alexander Herbig, Alexander Hübner, Christina Warinner

bioRxiv 871533; doi: 10.1101/871533


MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics

Leon Bichmann, Annika Nelde, Michael Ghosh, Lukas Heumos, Christopher Mohr, Alexander Peltzer, Leon Kuchenbecker, Timo Sachsenberg, Juliane S. Walz, Stefan Stevanović, Hans-Georg Rammensee, and Oliver Kohlbacher

Journal of Proteome Research 18(11), 3876-3884 (2019) doi: 10.1021/acs.jproteome.9b00313


LncPipe: A Nextflow-based pipeline for identification and analysis of long non-coding RNAs from RNA-Seq data.

Qi Zhao, Yu Sun, Dawei Wang, Hongwan Zhang, Kai Yu, Jian Zheng, Zhixiang Zuo.

Journal of Genetics and Genomics 20;45(7):399-401 (2018) doi: 10.1016/j.jgg.2018.06.005