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nano-rave: Citations

nano-rave

Sophia T. Girgis, Edem Adika, Felix E. Nenyewodey, Dodzi K. Senoo Jnr, Joyce M. Ngoi, Kukua Bandoh, Oliver Lorenz, Guus van de Steeg, Sebastian Nsoh, Kim Judge, Richard D. Pearson, Jacob Almagro-Garcia, Samirah Saiid, Solomon Atampah, Enock K. Amoako, Collins M. Morang’a, Victor Asoala, Elrmion S. Adjei, William Burden, William Roberts-Sengier, Eleanor Drury, Sónia Gonçalves, Gordon A. Awandare, Dominic P. Kwiatkowski, Lucas N. Amenga-Etego, William L. Hamilton. Nanopore sequencing for real-time genomic surveillance of Plasmodium falciparum. bioRxiv 521122; doi: 10.1101/521122

nf-core/nanoseq

Chen Y, Davidson NM, Wan YK, Patel H, Yao F, Low HM, Hendra C, Watten L, Sim A, Sawyer C, Iakovleva V, Lee PL, Xin L, Ng HEV, Loo JM, Ong X, Ng HQA, Wang J, Koh WQC, Poon SYP, Stanojevic D, Tran H-D, Lim KHE, Toh SY, Ewels PA, Ng H-H, Iyer N.G, Thiery A, Chng WJ, Chen L, DasGupta R, Sikic M, Chan Y-S, Tan BOP, Wan Y, Tam WL, Yu Q, Khor CC, Wüstefeld T, Pratanwanich PN, Love MI, Goh WSS, Ng SB, Oshlack A, Göke J, SG-NEx consortium. A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines. bioRxiv 610741. doi: 10.1101/610741

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

  • 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.

  • Clair3

    Zheng Z, Li S, Su J, Leung A W-S, Lam T-W, Luo R. Symphonizing pileup and full-alignment for deep learning-based long-read variant calling. Nature Computational Science. 2022;2(12):797–803. doi: 10.1038/s43588-022-00387-x. bioRxiv 474431

  • 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

  • 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.

  • pycoQC

    Leger A, Leonardi T. pycoQC, interactive quality control for Oxford Nanopore Sequencing. Journal of Open Source Software. 2019;4(34):1236. doi: 10.21105/joss.01236

  • 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.