For genus-level TE-annotation

oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/

GNU General Public License v3.0

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For genus-level TE-annotation #131

Closed LeeYEAH2 closed 1 year ago

LeeYEAH2 commented 1 year ago

Dear Shujun, LTR_retriever is a great tool to combine harvest&finder results, but the TE_annotation procedure could only classify Ltrs as Copia/Gypsy/unknown, I am wondering if it's possible to classify those Ltrs into genus level e.g. CRM/Galadriel for Gypsy. Do you have any idea on where to modify the code to fulfill this need? maybe the annotate_TE.pl part? With regards.

oushujun commented 1 year ago

Yes: https://academic.oup.com/hr/article/doi/10.1093/hr/uhac017/6532211?login=true

LeeYEAH2 commented 1 year ago

The work of LTR_retriever and TEsorter really helps. Thanks a lot .