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nf-core/genomeannotator: 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

  • Miniprot

    Li H, Protein-to-genome alignment with miniprot, Bioinformatics. 2023 Jan 1;39(1):btad014. doi: 10.1093/bioinformatics/btad014. PubMed PMID: 36648328

  • 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.

  • AUGUSTUS

    Stanke M, Diekhans M, Baertsch R and Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. doi: 10.1093/bioinformatics/btn013. Epub 2008 Jan 24.

  • Trinity

    Grabherr MG, Haas BJ, Yassour M, ... and Aviv Regev. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883.

  • PASA

    Haas BJ, Delcher AL, Mount SM, ... and Owen White. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 2003 Oct 1;31(19):5654-66. doi: 10.1093/nar/gkg770.

  • EvidenceModeler

    Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR and Wortman JR. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 2008 Jan 11;9(1):R7. doi: 10.1186/gb-2008-9-1-r7.

  • RepeatMasker

    Smit AFA, Hubley R and Green P. RepeatMasker Open-4.0. 2013-2015 http://www.repeatmasker.org.

  • RepeatModeler

    Smit AFA and Hubley R. RepeatModeler Open-1.0.2008-2015 http://www.repeatmasker.org.

  • FastP

    Chen S, Zhou Y, Chen Y and Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560.

  • STAR

    Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M and Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.

  • Infernal

    Nawrocki EP and Eddy SR. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013 Nov 15;29(22):2933-5. doi: 10.1093/bioinformatics/btt509. Epub 2013 Sep 4.

  • RFam

    Kalvari I, Nawrocki EP, Ontiveros-Palacios N, ... and Petrov AI. Rfam 14: expanded coverage of metagenomic, viral and microRNA families. Nucleic Acids Res. 2021 Jan 8;49(D1):D192-D200. doi: 10.1093/nar/gkaa1047.

  • Satsuma2

    Grabherr MG, Russell P, Meyer M, Mauceli E, Alföldi J, Di Palma F and Lindblad-Toh K. Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics. 2010 May 1;26(9):1145-51. doi: 10.1093/bioinformatics/btq102. Epub 2010 Mar 5.

  • Kraken

    Zamani N, Sundström G, Meadows JRS, Hoeppner MP, Dainat J, Lantz H, Haas BJ and Grabherr MG. A universal genomic coordinate translator for comparative genomics. BMC Bioinformatics. 2014 Jun 30;15:227. doi: 10.1186/1471-2105-15-227.

  • SPALN

    Gotoh O. A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence. Nucleic Acids Res. 2008 May;36(8):2630-8. doi: 10.1093/nar/gkn105. Epub 2008 Mar 15.

  • Minimap2

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

  • Samtools

    Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM and Li H. Twelve years of SAMtools and BCFtools. Gigascience. 2021 Feb 16;10(2):giab008. doi: 10.1093/gigascience/giab008.

  • Deeptools

    Ramírez F, Ryan DP, Grüning B, ... and Manke T. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5. doi: 10.1093/nar/gkw257. Epub 2016 Apr 13.

  • EggNOG-mapper

    Cantalapiedra CP, Hernandez-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Molecular Biology and Evolution. 2021. https://doi.org/10.1093/molbev/msab293

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.