├── .gitignore ├── .idea ├── .gitignore ├── .name ├── SPART.iml ├── SPART.py ├── inspectionProfiles │ ├── Project_Default.xml │ └── profiles_settings.xml ├── misc.xml ├── modules.xml ├── vcs.xml └── workspace.xml ├── .readthedocs.yaml ├── 00_Contig_screen ├── chloroplast.paf ├── chloroplast.txt ├── fastp.sh ├── flye.sh ├── gemma_los.py ├── hifiasm.sh ├── mitochondrion.paf ├── mitochondrion.txt ├── rm_mt_cp.sh └── verkko.sh ├── 01_Contig_scaffolding ├── Bionano_DLS_map.sh ├── HiC-Pro.sh ├── hicpro_config.txt └── yahs.sh ├── 02_Gap_patching ├── Centromeric_region_analysis.sh ├── chip-seq.py ├── paf_filter.pl ├── renameagp.pl └── wfmash_ragtag.sh ├── 03_Polishing ├── bwa_winnowmap.py ├── callsv_snv.py ├── calsv_snv.sh ├── clust.json ├── clust_align.json ├── conf_ck.yaml └── conf_ck_align.yaml ├── 04_Evaluation ├── BUSCO.sh ├── bac.sh ├── ltr.sh ├── mapping_rates_coverages .sh ├── qv.sh ├── synteny.sh ├── while.sh └── winnowmap.sh ├── 05_Annotation ├── Snakefile ├── clust.json ├── config.yaml └── modules │ ├── __pycache__ │ ├── fasta.cpython-310.pyc │ ├── fasta.cpython-35.pyc │ ├── fasta.cpython-39.pyc │ ├── mygff.cpython-310.pyc │ └── mygff.cpython-35.pyc │ ├── fasta.py │ └── mygff.py ├── LICENSE ├── README.md ├── SPART.py ├── SPART.yaml ├── clust.json ├── conf_ck.yaml ├── contacts.md ├── docs ├── Makefile ├── badge.html ├── make.bat └── source │ ├── README.md │ ├── README1.md │ ├── conf.py │ ├── index.rst │ ├── pipeline.jpg │ └── requirements.txt ├── example ├── README.md ├── cp │ └── chloroplast.fasta ├── mt │ └── mitochondrion.fasta ├── pcr │ ├── PCRFREE_1.fq │ └── PCRFREE_2.fq ├── rule.svg └── verkko │ └── verkko.fasta └── pic ├── pipeline.jpg └── rule.png /.gitignore: -------------------------------------------------------------------------------- 1 | docs/build/ 2 | -------------------------------------------------------------------------------- /.idea/.gitignore: -------------------------------------------------------------------------------- 1 | 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