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Abstract The amount of data produced by genome sequencing experiments has been growing rapidly over the past several years, making compression important for efficient storage, transfer and analysis of the data. In recent years, nanopore sequencing technologies have seen increasing adoption since they are portable, real-time and provide long reads. However, there has been limited progress on compression of nanopore sequencing reads obtained in FASTQ files since most existing tools are either general-purpose or specialized for short read data. We present NanoSpring, a reference-free compressor for nanopore sequencing reads, relying on an approximate assembly approach. We evaluate NanoSpring on a variety of datasets including bacterial, metagenomic, plant, animal, and human whole genome data. For recently basecalled high quality nanopore datasets, NanoSpring, which focuses only on the base sequences in the FASTQ file, uses just 0.35–0.65 bits per base which is 3–6$$\times$$ lower than general purpose compressors like gzip. NanoSpring is competitive in compression ratio and compression resource usage with the state-of-the-art tool CoLoRd while being significantly faster at decompression when using multiple threads (> 4$$\times$$ faster decompression with 20 threads). NanoSpring is available on GitHub athttps://github.com/qm2/NanoSpring.
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This content will become publicly available on December 1, 2025
The mechanical and sensory signature of plant-based and animal meat
Abstract Eating less meat is associated with a healthier body and planet. Yet, we remain reluctant to switch to a plant-based diet, largely due to the sensory experience of plant-based meat. Food scientists characterize meat using a double compression test, which only probes one-dimensional behavior. Here we use tension, compression, and shear tests–combined with constitutive neural networks–to automatically discover the behavior of eight plant-based and animal meats across the entire three-dimensional spectrum. We find that plant-based sausage and hotdog, with stiffnesses of 95.9 ± 14.1 kPa and 38.7 ± 3.0 kPa, successfully mimic their animal counterparts, with 63.5 ± 45.7 kPa and 44.3 ± 13.2 kPa, while tofurky is twice as stiff, and tofu is twice as soft. Strikingly, a complementary food tasting survey produces in nearly identical stiffness rankings for all eight products (ρ= 0.833,p = 0.015). Probing the fully three-dimensional signature of meats is critical to understand subtle differences in texture that may result in a different perception of taste. Our data and code are freely available athttps://github.com/LivingMatterLab/CANN
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- Award ID(s):
- 2320933
- PAR ID:
- 10601102
- Publisher / Repository:
- Springer
- Date Published:
- Journal Name:
- npj Science of Food
- Volume:
- 8
- Issue:
- 1
- ISSN:
- 2396-8370
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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