huntPalindrome

Find palindrome/large-scale-inverted-repeats in contigs/scaffolds/genomes

Usage

./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]

OUTPUT FORMAT

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