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Add support to LTR_STRUC, MGEScan 3.0.0, and LtrDetector!
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@oushujun oushujun released this 09 May 17:16
· 123 commits to master since this release
v2.6
05fe234

Support three more LTR programs!

Three more programs are supported by LTR_retriever:

Users need to convert candidates identified by these programs into the LTRharvest format with scripts located in the /bin folder:

  • convert_ltr_struc.pl
  • convert_MGEScan3.0.pl
  • convert_ltrdetector.pl

Then feed them to LTR_retriever with -inharvest. You may concatenate multiple LTRharvest format input files together.

Note: You won't find a lot of intact LTR elements from LTR_STRUC and LtrDetector outputs due to the fuzzy sequence boundaries these programs provided. So please use these two as supplements to other inputs.

Minor bug fix

  1. Fix the bug that would count 1 extra bit for sequence names
  2. Maintain codes for solo LTR identification and solo-intact ratio calculations: bin/solo_finder.pl and bin/intact_finder_coarse.pl (#41)
  3. Format sequence names in the redundant library output
  4. Add detailed notes to fix the conda RepeatMasker issue. Notes can be found here: #43
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