Find palindrome/large-scale-inverted-repeats in contigs/scaffolds/genomes
./huntPalindrome.sh -d /home/jitendra/myTools/huntPalindrome/test -g testPal.fa -t 1 -r normal -s 10000 -m all
-d Absolute path of directory
-g genome file name / should be in directory
-t threshold / keep it 1 -- not used by now
-r rule for synteny [strict/normal]
-s synteny resolution / best at 10000
-m mode of reporting [inverted/direct/all]
-v visualize with circos [yes/no]
huntPalindrome outfile columns: final.combined
- REF_CHROM <Reference entry chromosome name
- RPO_NAME <Name of the program used
- DETAIL <Detail of program
- REF_START <Reference start boundary estimate
- REF_END <Reference end boundary estimate
- REF_STRAND <Reference block strand
- REF_BLOCK <Reference synteny blocks number
- TAR_CHR <Targer chromosome name
- TAR_START <Target start location
- TAR_END <Target end location
- TAR_STRAND <Targer block strand
- TAR_BLOCK <Targer block number
- REPEATS <Detail information about the repeats
huntPalindrome result stats columns: final.stat
- TYPE <Type of repeats
- BLOCK_COUNT <Number of blocks
- BLOCK_SIZE <Size of repeats blocks
- GENOME_SIZE <Size of the genome
- PERCENTAGE <Percentage of bases in direct/indirect repeats