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424 Reviews — GigaScience — All Subjects

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Improving the Reliability and Quality of Nextflow Pipelines with nf-test
Forer, L., Schoenherr, S.
10.1101/2024.05.25.595877 — Posted: 2024-05-30 — 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
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
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
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
Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes
Bagci, C., Negri, T., Buena-Atienza, E., Gross, C., Ossowski, S., Ziemert, N.
10.1101/2025.05.28.656579 — Posted: 2025-05-28 — 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
TinkerHap - A Novel Read-Based Phasing Algorithm with Integrated Multi-Method Support for Enhanced Accuracy
Hartmann, U., Shaham, E., Nathan, D., Blech, I., Zeevi, D.
10.1101/2025.02.16.638517 — Posted: 2025-02-20 — Discussion: 2025-10-30  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
A high-quality reference genome for the Ural Owl (Strix uralensis) enables investigations of cell cultures as a genomic resource for endangered species
Chrysostomakis, I., Mozer, A., Bruno Di-Nizo, C., Fischer, D., Sargheini, N., von der Mark, L., Huettel, B., Astrin, J. J., Toepfer, T., Boehne, A.
10.1101/2025.01.22.633903 — Posted: 2025-01-24 — Discussion: 2025-09-30  GigaScience

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