├── 00haploid_pipeline ├── 00Assembly_validation.sh ├── 01Assembly_improvement.sh ├── README.md └── scripts │ ├── 01depth_span_gaps.pl │ ├── 02filter_depth_span_gaps.pl │ ├── 03filter_megablast.pl │ ├── 04split_genome.pl │ ├── 05check_scaf_with_marker.pl │ ├── 06get_gap_and_fragCov.pl │ ├── 07merge_anchored_scaf.pl │ ├── 08merge_unplaced_scaf.pl │ ├── 20k_processing.pl │ ├── 8k_processing.pl │ ├── GapCloser_with_mummer.pl │ ├── GetSeqFromGTF.pl │ └── gtf2gff3.pl ├── 01diploid_pipeline ├── 00Assembly_validation.sh ├── 01Assembly_improvement.sh ├── README.md └── scripts │ ├── 01parse_megablast.pl │ └── GapCloser_diploid_assembly_Mummer.pl ├── README.md └── resource ├── 20K_SNP_MARKERS.MAP.dat ├── 20K_SNP_MARKERS.dat ├── 20k.snp.fa ├── 20k_map_dist.txt ├── 8K_SNP.fa ├── 8K_SNP_LineageGroup.dat └── 8k_map_dist.txt /00haploid_pipeline/00Assembly_validation.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/00haploid_pipeline/00Assembly_validation.sh -------------------------------------------------------------------------------- /00haploid_pipeline/01Assembly_improvement.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/00haploid_pipeline/01Assembly_improvement.sh -------------------------------------------------------------------------------- /00haploid_pipeline/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/00haploid_pipeline/README.md -------------------------------------------------------------------------------- /00haploid_pipeline/scripts/01depth_span_gaps.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/00haploid_pipeline/scripts/01depth_span_gaps.pl -------------------------------------------------------------------------------- /00haploid_pipeline/scripts/02filter_depth_span_gaps.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/00haploid_pipeline/scripts/02filter_depth_span_gaps.pl -------------------------------------------------------------------------------- /00haploid_pipeline/scripts/03filter_megablast.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/00haploid_pipeline/scripts/03filter_megablast.pl -------------------------------------------------------------------------------- /00haploid_pipeline/scripts/04split_genome.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/00haploid_pipeline/scripts/04split_genome.pl -------------------------------------------------------------------------------- /00haploid_pipeline/scripts/05check_scaf_with_marker.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/00haploid_pipeline/scripts/05check_scaf_with_marker.pl -------------------------------------------------------------------------------- /00haploid_pipeline/scripts/06get_gap_and_fragCov.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/00haploid_pipeline/scripts/06get_gap_and_fragCov.pl -------------------------------------------------------------------------------- /00haploid_pipeline/scripts/07merge_anchored_scaf.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/00haploid_pipeline/scripts/07merge_anchored_scaf.pl -------------------------------------------------------------------------------- /00haploid_pipeline/scripts/08merge_unplaced_scaf.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/00haploid_pipeline/scripts/08merge_unplaced_scaf.pl -------------------------------------------------------------------------------- /00haploid_pipeline/scripts/20k_processing.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/00haploid_pipeline/scripts/20k_processing.pl -------------------------------------------------------------------------------- /00haploid_pipeline/scripts/8k_processing.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/00haploid_pipeline/scripts/8k_processing.pl -------------------------------------------------------------------------------- /00haploid_pipeline/scripts/GapCloser_with_mummer.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/00haploid_pipeline/scripts/GapCloser_with_mummer.pl -------------------------------------------------------------------------------- /00haploid_pipeline/scripts/GetSeqFromGTF.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/00haploid_pipeline/scripts/GetSeqFromGTF.pl -------------------------------------------------------------------------------- /00haploid_pipeline/scripts/gtf2gff3.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/00haploid_pipeline/scripts/gtf2gff3.pl -------------------------------------------------------------------------------- /01diploid_pipeline/00Assembly_validation.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/01diploid_pipeline/00Assembly_validation.sh -------------------------------------------------------------------------------- /01diploid_pipeline/01Assembly_improvement.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/01diploid_pipeline/01Assembly_improvement.sh -------------------------------------------------------------------------------- /01diploid_pipeline/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/01diploid_pipeline/README.md -------------------------------------------------------------------------------- /01diploid_pipeline/scripts/01parse_megablast.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/01diploid_pipeline/scripts/01parse_megablast.pl -------------------------------------------------------------------------------- /01diploid_pipeline/scripts/GapCloser_diploid_assembly_Mummer.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/01diploid_pipeline/scripts/GapCloser_diploid_assembly_Mummer.pl -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/README.md -------------------------------------------------------------------------------- /resource/20K_SNP_MARKERS.MAP.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/resource/20K_SNP_MARKERS.MAP.dat -------------------------------------------------------------------------------- /resource/20K_SNP_MARKERS.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/resource/20K_SNP_MARKERS.dat -------------------------------------------------------------------------------- /resource/20k.snp.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/resource/20k.snp.fa -------------------------------------------------------------------------------- /resource/20k_map_dist.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/resource/20k_map_dist.txt -------------------------------------------------------------------------------- /resource/8K_SNP.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/resource/8K_SNP.fa -------------------------------------------------------------------------------- /resource/8K_SNP_LineageGroup.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/resource/8K_SNP_LineageGroup.dat -------------------------------------------------------------------------------- /resource/8k_map_dist.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XuepengSun/apple_diploid_genomes/HEAD/resource/8k_map_dist.txt --------------------------------------------------------------------------------