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nf-core/nanoseq: 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.

SGNEx

Chen, Y., Davidson, N. M., Wan, Y. K., Patel, H., Yao, F., Low, H. M., ... & SG-NEx consortium. (2021). A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines. BioRxiv, 2021-04.

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

  • bambu

    Chen, Y., Sim, A. D., Wan, Y. K., Yeo, K., Lee, J. J. X., Ling, M. H., ... & Göke, J. (2022). Context-aware transcript quantification from long read RNA-seq data with Bambu. bioRxiv, 2022-11.

  • BEDTools

    Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.

  • cuteSV

    Jiang T, Liu Y, Jiang Y, Li J, Gao Y, Cui Z, Liu Y, Liu B, Wang Y. Long-read-based human genomic structural variation detection with cuteSV. Genome Biol. 2020 Aug 3;21(1):189. doi: 10.1186/s13059-020-02107-y. PMID: 32746918; PMCID: PMC7477834.

  • DeepVariant

    Poplin R, Chang PC, Alexander D, Schwartz S, Colthurst T, Ku A, Newburger D, Dijamco J, Nguyen N, Afshar PT, Gross SS, Dorfman L, McLean CY, DePristo MA. A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol. 2018 Nov;36(10):983-987. doi: 10.1038/nbt.4235. Epub 2018 Sep 24. PMID: 30247488.

  • featureCounts

    Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1;30(7):923-30. doi: 10.1093/bioinformatics/btt656. Epub 2013 Nov 13. PubMed PMID: 24227677.

  • GraphMap

    Sović I, Šikić M, Wilm A, Fenlon SN, Chen S, Nagarajan N. Fast and sensitive mapping of nanopore sequencing reads with GraphMap. Nat Commun. 2016 Apr 15;7:11307. doi: 10.1038/ncomms11307. PMID: 27079541; PMCID: PMC4835549.

  • JAFFAL

    Davidson NM, Chen Y, Sadras T, Ryland GL, Blombery P, Ekert PG, Göke J, Oshlack A. JAFFAL: detecting fusion genes with long-read transcriptome sequencing. Genome Biol. 2022 Jan 6;23(1):10. doi: 10.1186/s13059-021-02588-5. PMID: 34991664; PMCID: PMC8739696.

  • m6anet

    Hendra, C., Pratanwanich, P. N., Wan, Y. K., Goh, W. S., Thiery, A., & Göke, J. (2022). Detection of m6A from direct RNA sequencing using a multiple instance learning framework. Nature Methods, 1-9. PMID: 36357692; PMCID: PMC9718678.

  • PEPPER-Margin-DeepVariant

    Shafin K, Pesout T, Chang PC, Nattestad M, Kolesnikov A, Goel S, Baid G, Kolmogorov M, Eizenga JM, Miga KH, Carnevali P, Jain M, Carroll A, Paten B. Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads. Nat Methods. 2021 Nov;18(11):1322-1332. doi: 10.1038/s41592-021-01299-w. Epub 2021 Nov 1. PMID: 34725481; PMCID: PMC8571015.

  • Minimap2

    Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018 Sep 15;34(18):3094-3100. doi: 10.1093/bioinformatics/bty191. PMID: 29750242; PMCID: PMC6137996.

  • Medaka

  • 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.

  • NanoLyse

    De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M., & Van Broeckhoven, C. (2018). NanoPack: visualizing and processing long-read sequencing data. Bioinformatics, 34(15), 2666-2669. PubMed PMID: 29547981; PubMed Central PMCID: PMC6061794.

  • NanoPlot

    De Coster W, D'Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018 Aug 1;34(15):2666-2669. doi: 10.1093/bioinformatics/bty149. PubMed PMID: 29547981; PubMed Central PMCID: PMC6061794.

  • qcat

  • SAMtools

    Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.

  • Sniffles

    Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, Schatz MC. Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods. 2018 Jun;15(6):461-468. doi: 10 1038/s41592-018-0001-7. Epub 2018 Apr 30. PMID: 29713083; PMCID: PMC5990442.

  • StringTie2

    Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2 Genome Biol. 2019 Dec 16;20(1):278. doi: 10.1186/s13059-019-1910-1. PubMed PMID: 31842956; PubMed Central PMCID: PMC6912988.

  • UCSC tools

    Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010 Sep 1;26(17):2204-7. doi: 10.1093/bioinformatics/btq351. Epub 2010 Jul 17. PubMed PMID: 20639541; PubMed Central PMCID: PMC2922891.

  • xPore

    Pratanwanich PN, Yao F, Chen Y, Koh CWQ, Wan YK, Hendra C, Poon P, Goh YT, Yap PML, Chooi JY, Chng WJ, Ng SB, Thiery A, Goh WSS, Göke J. Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore. Nat Biotechnol. 2021 Nov;39(11):1394-1402. doi: 10.1038/s41587-021-00949-w. Epub 2021 Jul 19. PMID: 34282325.

R packages

  • R

    R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.

  • bambu

    Chen Y, Goeke J, Wan YK (2020). bambu: Reference-guided isoform reconstruction and quantification for long read RNA-Seq data. R package version 1.0.0.

  • BSgenome

    Pagès H (2020). BSgenome: Software infrastructure for efficient representation of full genomes and their SNPs. doi: 10.18129/B9.bioc.BSgenome.

  • DESeq2

    Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. PubMed PMID: 25516281; PubMed Central PMCID: PMC4302049.

  • DEXSeq

    Anders S, Reyes A, Huber W. Detecting differential usage of exons from RNA-seq data. Genome Res. 2012 Oct;22(10):2008-17. doi: 10.1101/gr.133744.111. Epub 2012 Jun 21. PubMed PMID: 22722343; PubMed Central PMCID: PMC3460195.

  • DRIMSeq

    Nowicka M, Robinson MD. DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics. F1000Res. 2016 Jun 13;5:1356. doi: 10.12688/f1000research.8900.2. PubMed PMID: 28105305; PubMed Central PMCID: PMC5200948.

  • stageR

    Van den Berge K, Soneson C, Robinson MD, Clement L. stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage. Genome Biol. 2017 Aug 7;18(1):151. doi: 10.1186/s13059-017-1277-0. PubMed PMID: 28784146; PubMed Central PMCID: PMC5547545.

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

  • 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.