├── README.md └── scripts ├── 1_mapping_sunks ├── KmersPos.py ├── SUNKsharing.py ├── Snakemake.py ├── example_output │ ├── chr8_asat_ONT.kmers │ ├── reads.positions │ ├── reads_nodup.fa │ ├── reads_nodup.fa.fai │ └── shared_SUNKs.tbl ├── kmers.fofn ├── ont_reads.fasta └── runsnake.sh └── 2_tiling ├── SUNKintervals.py └── run_sharedSUNKs.sh /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glogsdon1/sunk-based_assembly/HEAD/README.md -------------------------------------------------------------------------------- /scripts/1_mapping_sunks/KmersPos.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glogsdon1/sunk-based_assembly/HEAD/scripts/1_mapping_sunks/KmersPos.py -------------------------------------------------------------------------------- /scripts/1_mapping_sunks/SUNKsharing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glogsdon1/sunk-based_assembly/HEAD/scripts/1_mapping_sunks/SUNKsharing.py -------------------------------------------------------------------------------- /scripts/1_mapping_sunks/Snakemake.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glogsdon1/sunk-based_assembly/HEAD/scripts/1_mapping_sunks/Snakemake.py -------------------------------------------------------------------------------- /scripts/1_mapping_sunks/example_output/chr8_asat_ONT.kmers: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glogsdon1/sunk-based_assembly/HEAD/scripts/1_mapping_sunks/example_output/chr8_asat_ONT.kmers -------------------------------------------------------------------------------- /scripts/1_mapping_sunks/example_output/reads.positions: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glogsdon1/sunk-based_assembly/HEAD/scripts/1_mapping_sunks/example_output/reads.positions -------------------------------------------------------------------------------- /scripts/1_mapping_sunks/example_output/reads_nodup.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glogsdon1/sunk-based_assembly/HEAD/scripts/1_mapping_sunks/example_output/reads_nodup.fa -------------------------------------------------------------------------------- /scripts/1_mapping_sunks/example_output/reads_nodup.fa.fai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glogsdon1/sunk-based_assembly/HEAD/scripts/1_mapping_sunks/example_output/reads_nodup.fa.fai -------------------------------------------------------------------------------- /scripts/1_mapping_sunks/example_output/shared_SUNKs.tbl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glogsdon1/sunk-based_assembly/HEAD/scripts/1_mapping_sunks/example_output/shared_SUNKs.tbl -------------------------------------------------------------------------------- /scripts/1_mapping_sunks/kmers.fofn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glogsdon1/sunk-based_assembly/HEAD/scripts/1_mapping_sunks/kmers.fofn -------------------------------------------------------------------------------- /scripts/1_mapping_sunks/ont_reads.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glogsdon1/sunk-based_assembly/HEAD/scripts/1_mapping_sunks/ont_reads.fasta -------------------------------------------------------------------------------- /scripts/1_mapping_sunks/runsnake.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glogsdon1/sunk-based_assembly/HEAD/scripts/1_mapping_sunks/runsnake.sh -------------------------------------------------------------------------------- /scripts/2_tiling/SUNKintervals.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glogsdon1/sunk-based_assembly/HEAD/scripts/2_tiling/SUNKintervals.py -------------------------------------------------------------------------------- /scripts/2_tiling/run_sharedSUNKs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/glogsdon1/sunk-based_assembly/HEAD/scripts/2_tiling/run_sharedSUNKs.sh --------------------------------------------------------------------------------