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442 Reviews — GigaScience — All Subjects

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On the path to reference genomes for all biodiversity: lessons learned and laboratory protocols created in the Sanger Tree of Life core laboratory over the first 2000 species
Howard, C., Denton, A., Jackson, B., Bates, A., Jay, J., Yatsenko, H., Raman, P. S., Thomas, A., Oatley, G., do Amaral, R. V., Göktan, Z. E., Gomez, J. P. N., Clayton Lucey, I., Sinclair, E., Quail, M. A., Blaxter, M., Howe, K., Lawniczak, M.
10.1101/2025.04.11.648334 — Posted: 2025-04-11 — Discussion: 2025-10-30  GigaScience
GFFx: A Rust-based suite of utilities for ultra-fast genomic feature extraction
Chen, B., Dongya, W., Zhang, G.
10.1101/2025.08.08.669426 — Posted: 2025-08-12 — Discussion: 2025-10-30  GigaScience
The enduring advantages of the SLOW5 file format for raw nanopore sequencing data
Gamaarachchi, H., Jenner, S., Samarakoon, H., Ferguson, J. M., Deveson, I. W.
10.1101/2025.06.30.662478 — Posted: 2025-07-04 — Discussion: 2025-10-30  GigaScience
GTestimate: Improving relative gene expression estimation in scRNA-seq using the Good-Turing estimator
Fahrenberger, M., Esk, C., von Haeseler, A.
10.1101/2024.07.02.601501 — Posted: 2024-07-03 — Discussion: 2025-10-30  GigaScience
Reproducible processing of TCGA regulatory networks
Fanfani, V., Shutta, K. H., Mandros, P., Fischer, J., Saha, E., Micheletti, S., Chen, C., Ben Guebila, M., Lopes-Ramos, C. M., Quackenbush, J.
10.1101/2024.11.05.622163 — Posted: 2024-11-07 — Discussion: 2025-10-30  GigaScience
CryoDataBot: a pipeline to curate cryoEM datasets for AI-driven structural biology
Xu, Q., Wu, L., Rebelo, M., Feng, S., Yu, X., Farheen, F., Kihara, D., Zhou, Z. H.
10.1101/2025.09.09.675185 — Posted: 2025-09-10 — Discussion: 2025-10-30  GigaScience
PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking
Nasr, E., Henger, A., Gruning, B., Zierep, P., Batut, B.
10.1101/2024.06.26.600753 — Posted: 2024-06-30 — Discussion: 2025-09-30  GigaScience
Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence
Arantes, L. S., Brown, T., De Panis, D., Whiting, S. D., LaCasella, E. L., Carvajal, G. A., Kennedy, A., Edmunds, D., Bentley, B. P., Balacco, J., Whelan, C., Jain, N., Tilley, T., O'Toole, B., Traore, P., Jarvis, E. D., Berry, O., Dutton, P. H., Komoroske, L. M., Mazzoni, C. J.
10.1101/2025.03.26.644878 — Posted: 2025-03-28 — Discussion: 2025-09-30  GigaScience
CNSistent integration and feature extraction from somatic copy number profiles
Streck, A., Schwarz, R. F.
10.1101/2024.12.23.630118 — Posted: 2024-12-23 — Discussion: 2025-09-30  GigaScience
Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing.
Chang, J. J.-Y., Yang, X., Teng, H., Reames, B., Corbin, V., Coin, L. J. M.
10.1101/2024.10.25.620206 — Posted: 2024-10-25 — Discussion: 2025-09-30  GigaScience

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