example case

Prepare

Make sure you have already built this software, if not, try

cd ../ && make 

Run

run with racon

../TGS-GapCloser.sh --scaff input.scaff.fasta --reads ont.reads.fasta --output test_racon --racon YOUR-RACON-FILE

run with pilon

../TGS-GapCloser.sh --scaff input.scaff.fasta --reads ont.reads.fasta --output test_pilon --ngs ngs.reads.fastq  \
	--pilon  pilon-path/pilon-1.23.jar  \
        --samtools samtools-path/bin/samtools  \
        --java    java-path/bin/java \

run without error-correction

../TGS-GapCloser.sh --scaff input.scaff.fasta --reads ont.reads.fasta --output test_ne --ne