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number-25/LongTranscriptomics: 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

  • nanoq

    Steinig et al., (2022). Nanoq: ultra-fast quality control for nanopore reads. Journal of Open Source Software, 7(69), 2991, https://doi.org/10.21105/joss.02991

  • SEQUALI

    Ruben H P Vorderman, Sequali: efficient and comprehensive quality control of short- and long-read sequencing data, Bioinformatics Advances, Volume 5, Issue 1, 2025, vbaf010, https://doi.org/10.1093/bioadv/vbaf010

  • minimap2

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

  • samtools

    Li, Heng, et al. "The sequence alignment/map format and SAMtools." bioinformatics 25.16 (2009): 2078-2079.

  • bedtools

    Quinlan, Aaron R., and Ira M. Hall. "BEDTools: a flexible suite of utilities for comparing genomic features." Bioinformatics 26.6 (2010): 841-842.

  • cramino

    Wouter De Coster, Rosa Rademakers, NanoPack2: population-scale evaluation of long-read sequencing data, Bioinformatics, Volume 39, Issue 5, May 2023, btad311, https://doi.org/10.1093/bioinformatics/btad311

  • alfred

    Rausch, T., Fritz, M.H., Korbel, J.O. and Benes, V. Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing. Bioinformatics. 2019 Jul 15;35(14):2489-2491. https://doi.org/10.1093/bioinformatics/bty1007

  • ngs-bits

    Marc Sturm, et al. Imgag/ngs-bits: 2025_09. 2025_09, Zenodo, 25 Sept. 2025, https://doi.org/10.5281/zenodo.17201254.

  • FLAIR

    Tang, Alison D., et al. "Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns." Nature communications 11.1 (2020): 1438.

  • bambu

    Chen, Ying, et al. "Context-aware transcript quantification from long-read RNA-seq data with Bambu." Nature methods 20.8 (2023): 1187-1195.

  • IsoQuant

    Prjibelski, Andrey D., et al. "Accurate isoform discovery with IsoQuant using long reads." Nature Biotechnology 41.7 (2023): 915-918.

  • StringTie

    Kovaka, Sam, et al. "Transcriptome assembly from long-read RNA-seq alignments with StringTie2." Genome biology 20.1 (2019): 278.

  • gffcompare

    Pertea, Geo, and Mihaela Pertea. "GFF utilities: GffRead and GffCompare." F1000Research 9 (2020): ISCB-Comm.

  • oarfish

    Zare Jousheghani, Zahra, Noor Pratap Singh, and Rob Patro. "Oarfish: Enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification." Bioinformatics 41.Supplement_1 (2025): i304-i313.

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.