#This is the walkstrough how to identifiy genome-wide synteny markers based on LASTZ alignment.
Step1：Mask the repeat sequences for both genomes and chromosomes.
RepeatMasker -pa 40 -nolow -norna -gff -xmall -lib custom.TE.lib_for_rice.fa AAChr1.txt RepeatMasker -pa 40 -nolow -norna -gff -xmall -lib custom.TE.lib_for_FF.fa FFChr1.txt
Step2: Alignment using LASTZ and Chain/Net
lastz AAChr1.txt FFChr1.txt K=2200 L=6000 Y=3400 E=30 H=0 O=400 T=1 --format=axt --out=chr01.axt axtChain -linearGap=medium chr01.axt AAChr1.txt FFChr1.txt chr01.axt.chain chainPreNet chr01.axt.chain AAChr1.txt.sizes FFChr1.txt.sizes chr01.chain.filter chainNet chr01.chain.filter -minSpace=1 AAChr1.txt.sizes FFChr1.txt.sizes chr1.chain.filter.tnet chr1.chain.filter.qnet netSyntenic chr1.chain.filter.tnet chr1.chain.filter.tnet.synnet netToAxt chr1.chain.filter.tnet.synnet chr1.chain.filter.tnet.synnet chr01.chain.filter AAChr1.txt FFChr1.txt chr1.chain.filter.tnet.synnet.axt axtSort chr1.chain.filter.tnet.synnet.axt chr1.chain.filter.tnet.synnet.Sort.axt axtToMaf chr1.chain.filter.tnet.synnet.axt AAChr1.txt.sizes FFChr1.txt.sizes -tPrefix=target. -qPrefix=query. chr1.chain.filter.tnet.synnet.axt.maf
Step 3: Get syntenic markers
perl Maf2rawsynteny.pl chr1.chain.filter.tnet.synnet.axt.maf target.AAChr1 query.FFChr1
perl Get_synteny.pl -i chr1.chain.filter.tnet.synnet.axt.maf -n 0 -m 3 -t target.AAChr1 -q query.FFChr1 -o syn.final.out
@ https://github.com/yiliao1022/Centromere_synteny_project
