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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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LTRharvest as input #22

Closed xinshuaiqi closed 5 years ago

xinshuaiqi commented 5 years ago

Hi Shujun, I notice the updated Readme file now suggest using "LTRharvest" as input file. Are there any reason LTR_finder no longer preferred? Is the result based on solo LTRharvest robust enough?

oushujun commented 5 years ago

Hi Xinshuai,

The line you were suggesting in the ReadMe is just an example to run LTR_retriever. Please refer to the full usage in the manual pdf. It is still recommended to use both LTRharvest and LTR_finder as raw input to improve the LTR library sensitivity (marginally, though, please refer to the supplementary table for this margin) for the purpose of whole-genome LTR annotation. For the use of LAI, it is strongly recommended to use both inputs to fully identify intact LTR-RTs, otherwise the resulting LAI could drop a couple points.

Shujun