Pinned Repositories
GraffiTE
GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
hifiasm
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
GuppyGeneDuplication
Scripts for Lin, Y., Darolti, I., Furman, B. L. F., Almeida, P., Sandkam, B. A., et al., Breden, F., Wright, A. E., Mank, J. E. (2022) Gene duplication to the Y chromosome in Trinidadian Guppies. Molecular Ecology. https://doi.org/10.1111/mec.16355
GuppyGermlineDNMs
Scripts for Lin, Y., Darolti, I., van der Bijl, W., Morris, J., Mank, J. E. (2023) Extensive variation in germline de novo mutations in Poecilia reticulata. Genome Research
lin-yuying.github.io
NextPolish2
Repeat-aware polishing genomes assembled using HiFi long reads
Lin-Yuying's Repositories
Lin-Yuying/GuppyGeneDuplication
Scripts for Lin, Y., Darolti, I., Furman, B. L. F., Almeida, P., Sandkam, B. A., et al., Breden, F., Wright, A. E., Mank, J. E. (2022) Gene duplication to the Y chromosome in Trinidadian Guppies. Molecular Ecology. https://doi.org/10.1111/mec.16355
Lin-Yuying/GuppyGermlineDNMs
Scripts for Lin, Y., Darolti, I., van der Bijl, W., Morris, J., Mank, J. E. (2023) Extensive variation in germline de novo mutations in Poecilia reticulata. Genome Research
Lin-Yuying/lin-yuying.github.io