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.plwas 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.pyidentified 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.plclassified the SNP phased blocks into sex-specific block. - Step 4:
The fourth one
4.filterBLOCK_reads.pyfiltered 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.