Repeat Library Construction - O.lurida RepeatModeler v1.0.11

In further attempts to improve our Ostrea lurida genome annotation, I decided to generate a species-specific repeat library for use with MAKER genome annotation using RepeatModeler.

Ran on both versions of our O.lurida genome assemblies. Details on assemblies can be found on our [Genomic Resources wiki (GitHub)(https://github.com/RobertsLab/resources/wiki/Genomic-Resources#ostrea-lurida).

-[Olurida_v081.fa (only contigs >1000bp)(https://owl.fish.washington.edu/halfshell/genomic-databank/Olurida_v081.fa)

Tasks were run on Emu (Apple Xserve; Ubuntu 16.04). All operations were performed in the following Jupyter Notebook (GitHub):


RESULTS

Each run took ~1.5days to complete.

Output folders:

Repeats FastAs:

  • [Ostrea_lurida_v080-families.fa (1.3MB)(https://gannet.fish.washington.edu/Atumefaciens/20181022_Olurida_v080_repeatmodeler/Ostrea_lurida_v080-families.fa)

  • [Ostrea_lurida_v081-families.fa (1.3MB)(https://gannet.fish.washington.edu/Atumefaciens/20181022_Olurida_v081_repeatmodeler/Ostrea_lurida_v081-families.fa)

Will use these repeat libraries in subsequent MAKER genome annotations.