~ ~ ~ Run LTR_HARVEST in parallel ~ ~ ~

This is a Perl wrapper for LTR_harvest modified from LTR_FINDER_parallel. All rights reserved to the original authors.

Prerequisite: GenomeTools

conda create -n LTR_HARVEST_parallel
conda install -n LTR_HARVEST_parallel -c bioconda -y genometools-genometools
conda activate LTR_HARVEST_parallel

Installation of LTR_HARVEST_parallel: No need. Just download and run.

Usage: perl LTR_HARVEST_parallel -seq [file] -size [int] -overlap [int] -threads [int]  
Options:
	-seq    [file]  Specify the sequence file.
	-size   [int]   Specify the size you want to split the genome sequence.
			Please make it large enough to avoid spliting too many LTR elements. Default 5000000 (bp).  			 
	-overlap|-o        [int]   Specify the overlapping size for each split piece. Default 100000 (bp)
	-time   [int]   Specify the maximum time to run a subregion (a thread).
			This helps to skip simple repeat regions that take a substantial of time to run. Default: 120 (seconds).
			Increase -time when -size increased.  
	-try1   [0|1]   If a region requires more time than the specified -time (timeout), decide:  
				0, discard the entire region.
				1, further split to 50 Kb regions to salvage LTR candidates (default);
	-next           Only summarize the results for previous jobs without rerunning LTR_HARVEST (for -v).
	-verbose|-v     Retain LTR_HARVEST outputs for each sequence piece.
	-threads|-t     [int]   Indicate how many CPU/threads you want to run LTR_HARVEST.
	-check_dependencies Check if dependencies are fullfiled and quit
	-help|-h        Display this help information.

Input

Genome file in multi-FASTA format. The program will be automatically shortern the sequence ID by just keeping the string before the first space.

Output

GFF3, LTRharvest (STDOUT) formats of predicted LTR candidates.