Program, Pipeline Name or Method Name

LTRFinder, RepeatModeler, RepeatMasker, Bedtools Intersect

Program, Pipeline or Method version

LTR finder 1.05, Repeatmodeler 1.0.8, RepeatMasker 4.0.6, Bedtools 2.26.0

Source Name

Full length LTR models merged with bedtools. Only those that overlap with repeatmodeler repeats, merged with bed

Time Executed

April 6, 2018, midnight

Category

Genome structure

Description

A RepeatModeler library was created from the genome, which was subsequently used for masking with RepeatMasker. LTR pairs were identified in the genome with LTR Finder, followed by Bedtools merge to create proper overlaps for nested LTR's. Overlap between the two sets of output were identified with Bedtools intersect.

File

ltrretroelementsclassifiedcut_sorted.gff_.gz

Index

ltrretroelementsclassifiedcut_sorted.gff_.gz.tbi