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428 Reviews — GigaScience — All Subjects

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An improved pig reference genome sequence to enable pig genetics and genomics research

Warr, A., Affara, N., Aken, B., Beiki, H., Bickhart, D. M., Billis, K., Chow, W., Eory, L., Finlayson, H. A., Flicek, P., Giron, C. G., Griffin, D. K., Hall, R., Hannum, G., Hourlier, T., Howe, K., Hume, D. A., Izuogu, O., Kim, K., Koren, S., Liu, H., Manchanda, N., Martin, F. J., Nonneman, D. J., O'Connor, R. E., Phillippy, A. M., Rohrer, G. A., Rosen, B. D., Rund, L. A., Sargent, C. A., Schook, L. B., Schroeder, S. G., Schwartz, A. S., Skinner, B. M., Talbot, R., Tseng, E., Tuggle, C. K., Watson, M., Smith, T. P., Archibald, A. L.

10.1101/668921 — Posted: 2019-06-13 — Discussion: 2022-01-24 GigaScience

Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines

Dozmorov, M. G., Tyc, K. M., Sheffield, N. C., Boyd, D. C., Olex, A. L., Reed, J., Harrell, J. C.

10.1101/2020.10.17.343814 — Posted: 2020-10-17 — Discussion: 2022-01-24 GigaScience

Long-reads assembly of the Brassica napus reference genome, Darmor-bzh

Rousseau-Gueutin, M., Belser, C., Da Silva, C., Richard, G., Istace, B., Cruaud, C., Falentin, C., Boideau, F., Boutte, J., Delourme, R., Deniot, G., Engelen, S., Ferreira de Carvalho, J., Lemainque, A., Maillet, L., Morice, J., Wincker, P., Denoeud, F., Chevre, A.-M., Aury, J.-M.

10.1101/2020.07.22.215749 — Posted: 2020-07-22 — Discussion: 2022-01-24 GigaScience

Efficiently processing amplicon sequencing data for microbial ecology with dadasnake, a DADA2 implementation in Snakemake

Weissbecker, C., Schnabel, B., Heintz-Buschart, A.

10.1101/2020.05.17.095679 — Posted: 2020-05-19 — Discussion: 2022-01-24 GigaScience

Framework for determining accuracy of RNA sequencing data for gene expression profiling of single samples

Beale, H. C., Roger, J., Cattle, M., McKay, L., Learned, K., Lyle, G., Kephart, E., Currie, R., Lam, D. L., Sanders, L., Pfeil, J., Vivian, J., Bjork, I., Salama, S., Haussler, D., Vaske, O.

10.1101/716829 — Posted: 2019-07-30 — Discussion: 2022-01-24 GigaScience

Multi-Dimensional Machine Learning Approaches for Fruit Shape Recognition and Phenotyping in Strawberry

Feldmann, M. J., Hardigan, M. A., Famula, R. A., Lopez, C. M., Tabb, A., Cole, G. S., Knapp, S. J.

10.1101/736397 — Posted: 2019-08-15 — Discussion: 2022-01-24 GigaScience

Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements

Hosseini, M., Pratas, D., Morgenstern, B., Pinho, A. J.

10.1101/2019.12.23.887349 — Posted: 2019-12-25 — Discussion: 2022-01-24 GigaScience

A catalog of microbial genes from the bovine rumen reveals the determinants of herbivory

Li, J., Zhong, H., Ramayo-Caldas, Y., Terrapon, N., Lombard, V., Potocki-Veronese, G., Estelle-Fabrellas, J., Popova, M., Yang, Z., Zhang, H., Li, F., Tang, S., Chen, W., Chen, B., Li, J., Guo, J., Martin, C., Maguin, E., Xu, X., Yang, H., Wang, J., Madsen, L., Kristiansen, K., Henrissat, B., Ehrlich, S. D., Morgavi, D. P.

10.1101/272690 — Posted: 2018-02-27 — Discussion: 2022-01-24 GigaScience

Community Standards for Open Cell Migration Data

Gonzalez-Beltran, A. N., Masuzzo, P., Ampe, C., Bakker, G.-J., Besson, S., Eibl, R. H., Friedl, P., Gunzer, M., Kittisopikul, M., Le Devedec, S. E., Leo, S., Moore, J., Paran, Y., Prilusky, J., Rocca-Serra, P., Roudot, P., Schuster, M., Sergeant, G., Stromblad, S., Swedlow, J. R., van Erp, M., Van Troys, M., Zaritsky, A., Sansone, S.-A., Martens, L.

10.1101/803064 — Posted: 2019-10-14 — Discussion: 2022-01-24 GigaScience

Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American killifish from the Fundulus genus

Johnson, L. K., Sahasrabudhe, R., Gill, T., Roach, J. L., Froenicke, L., Brown, C. T., Whitehead, A.

10.1101/686246 — Posted: 2019-06-28 — Discussion: 2022-01-24 GigaScience