Rice pan genome analysis

Scripts for the analysis in the comparitive analysis of 70 rice species

01 pan TE database

Denovo TE identification with repeatmodler

02 annotation

pan TE database build script and TE identify

03 TE enrichment

Enriched TE entries and full length LTR identified

04 make full TE bed

Clustered LTR analysis

05 synteny of TE

06 SV analysis of CR

SV analysis around CR