Heterodera glycines v2 (Soybean Cyst Nematode (v2))
Program, Pipeline Name or Method Name:
Inverted Repeat Finder,Repeatmodeler, RepeatMasker, Bedtools
Program, Pipeline or Method version:
Inverted Repeat Finder (3.07), Repeatmodeler 1.0.8, RepeatMasker 4.0.6, Bedtools 2.26.0
Full length TIR pairs models merged with bedtools. Only those that overlap with repeatmodeler repeats, merged with bed
Materials & Methods (Description and/or Program Settings):
A RepeatModeler library was created from the genome, which was subsequently used for masking with RepeatMasker. TIR pairs were identified in the genome with Inverted Repeat Finder, followed by Bedtools merge to create proper overlaps for nested TIR's. Overlap between the two sets of output were identified with Bedtools intersect.