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simon19891216 / CentIER

BSD 3-Clause "New" or "Revised" License
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Accept exists scn file or LTR_retriever results #17

Open xiekunwhy opened 2 months ago

xiekunwhy commented 2 months ago

Hi,

ltr_finder, ltrharvest and LTR_retriever are quite slow in centier pipeline (expecially when the genome size is large), would please modify the code to accept existing scn file or LTR_retriever results, So that users can run ltr_finder, ltrharvest and LTR_retriever independently to speed up the whole pipeline.

Best, Kun

simon19891216 commented 2 months ago

Sorry for this. There is indeed an alternative method. As far as I know, the TRF and LTR_retriever software, which are frequently utilized in the assembly process, can be leveraged in this scenario. Therefore, if you already have the result files from these two programs, you may consider directly using their outputs as inputs to avoid running the programs again, thereby accelerating the analysis process. I will soon incorporate these two parameters into CentIER.

At 2024-08-27 21:08:00, "xiekunwhy" @.***> wrote:

Hi,

ltr_finder, ltrharvest and LTR_retriever are quite slow in centier pipeline (expecially when the genome size is large), would please modify the code to accept existing scn file or LTR_retriever results, So that users can run ltr_finder, ltrharvest and LTR_retriever independently to speed up the whole pipeline.

Best, Kun

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