sexPhase

A pipeline that was used to identify X-specific and Y-specific reads in Ficus hispida. The pipeline includes four scripts that are archived in the repo.

• Step 1: The first script 1.determineGeno.pl was used to determine which genotype belong to X chromosomes and which belong to Y chromosome based on re-sequenced male and female samples.
• Step 2: The second script 2.retrieveReads.py identified pacbio reads that could cover phased genotypes from whatshap program and classified them into different haplotypes.
• Step 3: The third one 3.identify_sex-phasedBLOCKs.pl classified the SNP phased blocks into sex-specific block.
• Step 4: The fourth one 4.filterBLOCK_reads.py filtered and outputed phased pacbio reads that could be assigned into X and Y chromosomes. These phased pacbio reads were further used to de novo assemble sex chromosomes.