It just gets better with community efforts!

Major Updates

1. Add TEsorter to help to identify not LTR sequences. Candidate LTRs will be determined as "false" if they contain not-LTR HMM profile matches even the candidate contains LTR/TSD and the TGCA motif. This purging will remove a small number of structurally intact LTR candidates (5/2304 in rice). This implementation offers slight improvements over older versions and should be more significant for larger genomes.

   LTR_retriever-harvest_FINDER	sens	spec	accu	prec	FDR	F1
   retriever_v2.5	0.967	0.920	0.931	0.789	0.211	0.869
   retriever_v2.6	0.963	0.931	0.939	0.811	0.189	0.881
   retriever_v2.9.2	0.966	0.926	0.935	0.802	0.198	0.876
   retriever_v2.9.4	0.967	0.928	0.937	0.804	0.196	0.878

2. Add more filtering parameters to identify solo LTRs, improve the solo-intact ratio calculation (#111, #110).

3. Resolve RMblast errors when it attempts to overutilize CPUs #137

Other improvements

1. Now require sequence IDs for 13 characters or less to accomodate for huge chromosomes up to 999Mb in length.
2. Add missing TRF parameter (#133)
3. Add check to ensure the input genome is writable (LTR_retriever won't overwrite your genome) (#125).
4. Remove gap length for genome size calculation.

Acknowledgements

Andreas Wallberg, @Shokusei, Evan Ernst, @xie-wei-hh, @with9, and users like YOU!