The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Scaling read aligners to hundreds of threads on general-purpose processors
Open accessAbstract
Motivation: General-purpose processors can now contain many dozens of processor cores and support hundreds of simultaneous threads of execution. To make best use of these threads, genomics software must contend with new and subtle computer architecture issues. We discuss some of these and propose methods for improving thread scaling in tools that analyze each read independently, such as read aligners. Results: We implement these methods in new versions of Bowtie, Bowtie 2 and HISAT. We greatly improve thread scaling in many scenarios, including on the recent Intel Xeon Phi architecture. We also highlight how bottlenecks are exacerbated by variable-record-length file formats like FASTQ and suggest changes that enable superior scaling. Availability and implementation: Experiments for this study: https://github.com/BenLangmead/bowtie-scaling. Bowtie: http://bowtie-bio.sourceforge.net . Bowtie 2: http://bowtie-bio.sourceforge.net/bowtie2 . HISAT: http://www.ccb.jhu.edu/software/hisat Supplementary information: Supplementary data are available at Bioinformatics online.
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Cites
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Chen, L., Zhernakova, D. V., Kurilshikov, A., Andreu-Sánchez, S., Wang, D., Augustijn, H. E., Vich Vila, A., Study, L. C., Weersma, R. K., Medema, M. H., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-02014-8 · Cited by 327
Transcription factors interact with RNA to regulate genes
Oksuz, O., Henninger, J. E., Warneford-Thomson, R., Zheng, M. M., Erb, H., Vancura, A., Overholt, K. J., Hawken, S. W., Banani, S. F., Lauman, R., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.06.012 · Cited by 275
Beresford-Jones, B. S., Forster, S. C., Stares, M. D., Notley, G., Viciani, E., Browne, H. P., Boehmler, D. J., Soderholm, A. T., Kumar, N., Vervier, K., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2021.12.003 · Cited by 194
A molecular glue degrader of the WIZ transcription factor for fetal hemoglobin induction
Ting, P. Y., Borikar, S., Kerrigan, J. R., Thomsen, N. M., Aghania, E., Hinman, A. E., Reyes, A., Pizzato, N., Fodor, B. D., Wu, F., et al. (2024) · Science · doi:10.1126/science.adk6129 · Cited by 97
Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic
Nelson, C. W., Ardern, Z., Goldberg, T. L., Meng, C., Kuo, C.-H., Ludwig, C., Kolokotronis, S.-O., & Wei, X. (2020) · eLife · doi:10.7554/elife.59633 · Cited by 87
Metadata
- Authors
- Langmead, B., Wilks, C., Antonescu, V., & Charles, R.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-07-18
- Volume
- 35
- Issue
- 3
- Pages
- 421-432
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2952597168
- Cited by
- 942
- References
- 8
- FWCI
- 15.15
- Type
- journal article
- Language
- en
- Open access
- hybrid
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