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nf-core/hadge: Citations

nf-core

Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

Nextflow

Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

Pipeline tools

Genetic-based deconvolution

  • Demuxlet

    Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, Wan E, Wong S, Byrnes L, Lanata CM, Gate RE, Mostafavi S, Marson A, Zaitlen N, Criswell LA, Ye CJ. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nat Biotechnol. 2018 Jan;36(1):89-94. doi: 10.1038/nbt.4042. Epub 2017 Dec 11. Erratum in: Nat Biotechnol. 2020 Nov;38(11):1356. doi: 10.1038/s41587-020-0715-9. PMID: 29227470; PMCID: PMC5784859.

  • Freemuxlet

Zhang, F. Leveraging genetic variants for rapid and robust upstream analysis of massive sequence data. (2019). [Doctoral Dissertation, University of Michigan] https://deepblue.lib.umich.edu/handle/2027.42/151524.

  • Souporcell

    Heaton H, Talman AM, Knights A, Imaz M, Gaffney DJ, Durbin R, Hemberg M, Lawniczak MKN. Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes. Nat Methods. 2020 Jun;17(6):615-620. doi: 10.1038/s41592-020-0820-1. Epub 2020 May 4. PMID: 32366989; PMCID: PMC7617080.

  • Vireo

    Huang Y, McCarthy DJ, Stegle O. Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference. Genome Biol. 2019 Dec 13;20(1):273. doi: 10.1186/s13059-019-1865-2. PMID: 31836005; PMCID: PMC6909514.

Hashing-based deconvolution

  • BFF

    Boggy GJ, McElfresh GW, Mahyari E, Ventura AB, Hansen SG, Picker LJ, Bimber BN. BFF and cellhashR: analysis tools for accurate demultiplexing of cell hashing data. Bioinformatics. 2022 May 13;38(10):2791-2801. doi: 10.1093/bioinformatics/btac213. PMID: 35561167; PMCID: PMC9113275.

  • Demuxem

    Gaublomme JT, Li B, McCabe C, Knecht A, Yang Y, Drokhlyansky E, Van Wittenberghe N, Waldman J, Dionne D, Nguyen L, De Jager PL, Yeung B, Zhao X, Habib N, Rozenblatt-Rosen O, Regev A. Nuclei multiplexing with barcoded antibodies for single-nucleus genomics. Nat Commun. 2019 Jul 2;10(1):2907. doi: 10.1038/s41467-019-10756-2. Erratum in: Nat Commun. 2020 Nov 2;11(1):5619. doi: 10.1038/s41467-020-19357-w. PMID: 31266958; PMCID: PMC6606589.

  • GMM-Demux

    Xin H, Lian Q, Jiang Y, Luo J, Wang X, Erb C, Xu Z, Zhang X, Heidrich-O'Hare E, Yan Q, Duerr RH, Chen K, Chen W. GMM-Demux: sample demultiplexing, multiplet detection, experiment planning, and novel cell-type verification in single cell sequencing. Genome Biol. 2020 Jul 30;21(1):188. doi: 10.1186/s13059-020-02084-2. PMID: 32731885; PMCID: PMC7393741.

  • HashedDrops

    Lun ATL, Riesenfeld S, Andrews T, Dao TP, Gomes T; participants in the 1st Human Cell Atlas Jamboree; Marioni JC. EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data. Genome Biol. 2019 Mar 22;20(1):63. doi: 10.1186/s13059-019-1662-y. PMID: 30902100; PMCID: PMC6431044.

  • Hashsolo

    Bernstein NJ, Fong NL, Lam I, Roy MA, Hendrickson DG, Kelley DR. Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning. Cell Syst. 2020 Jul 22;11(1):95-101.e5. doi: 10.1016/j.cels.2020.05.010. Epub 2020 Jun 26. PMID: 32592658.

  • HTODemux

    Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Chattopadhyay PK, Swerdlow H, Satija R, Smibert P. Simultaneous epitope and transcriptome measurement in single cells. Nat Methods. 2017 Sep;14(9):865-868. doi: 10.1038/nmeth.4380. Epub 2017 Jul 31. PMID: 28759029; PMCID: PMC5669064.

  • Multiseq

    McGinnis CS, Patterson DM, Winkler J, Conrad DN, Hein MY, Srivastava V, Hu JL, Murrow LM, Weissman JS, Werb Z, Chow ED, Gartner ZJ. MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices. Nat Methods. 2019 Jul;16(7):619-626. doi: 10.1038/s41592-019-0433-8. Epub 2019 Jun 17. PMID: 31209384; PMCID: PMC6837808.

Others

  • Cellsnp-lite

    Huang X, Huang Y. Cellsnp-lite: an efficient tool for genotyping single cells. Bioinformatics. 2021 Dec 7;37(23):4569-4571. doi: 10.1093/bioinformatics/btab358. PMID: 33963851.

  • MultiQC

    Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

Software packaging/containerisation tools

  • Anaconda

    Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

  • Bioconda

    Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

  • BioContainers

    da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

  • Docker

    Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

  • Singularity

    Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.