Code and pipelines for: A chromosome-scale reference genome for the Ural owl (Strix uralensis) demonstrates the applicability of cell cultures as a sources for genomics of endangered species

Treee structure of files: ├── 0.ASM ### Assemble long-read genome from HiFi (and Hi-C reads if available) For information on how to best run the pipeline, which parts to run first and how, how to set up the configuration file, etc see the README file ### │ ├── 00.SGE_genome_assembly.sh │ ├── compleasm.sh │ ├── README.md │ ├── config │ │ └── config.yaml │ ├── envs [...] │ ├── makefiles │ │ ├── BUSCO.smk │ │ ├── CCS_DEEPCONSENSUS.smk │ │ ├── DECONTAM.smk │ │ ├── FINAL_ASM_STATS.smk │ │ ├── FLYE.smk │ │ ├── HIC.smk │ │ ├── HIFIASM.smk │ │ ├── MERQURY.smk │ │ ├── PROCESS_HIC_READS.smk │ │ ├── PURGEDUPS.smk │ │ ├── STATS.smk │ │ └── VISUALIZE.smk │ └── snakefile.smk ├── 1.MAPPING_&_CONTACTS ### Scripts to map the final assembly to back to the HiC, HiFi and subreads to get quality statistics. Mapping to the HiC also allows the creation of HiC contact maps in these scripts (pretext for curation, HiCExplorer for visualization) ### │ ├── 00b.Mapping_HiFi_HiC_ASMs_contactmaps.smk │ ├── 05.SGE_mitomapping.sh │ └── pretext2asm_post_curation.sh ├── 3.EARLGREY │ └── 02.SGE_annot_earlgrey.sh ├── 4.PROTEIN_ANNOT ### Scripts to do repeat and protein annotation of genome. Edited from previous publication Repeat annotation part is replaced by EarlGrey.Protein annotation combines BRAKER and GALBA using TSEBRA to get the final gene annotation ### │ ├── BRAKER │ │ ├── config │ │ │ └── config.yaml │ │ ├── SGE_annot.sh │ │ └── workflow │ │ ├── envs [...] │ │ ├── rules │ │ │ ├── 01-repeat-masking.smk │ │ │ ├── 02-rnaseq-mapping-hisat.smk │ │ │ ├── 02-rnaseq-mapping.smk │ │ │ ├── 03-braker-run.smk │ │ │ └── 04-repeatlandscape.smk │ │ ├── scripts │ │ │ ├── fasta_split_1.pl │ │ │ └── repeat_to_gff.pl │ │ └── Snakefile.smk │ ├── GALBA │ │ └── run_galba.sh │ └── TSEBRA │ ├── edit_annotation_after_tsebra_braker.sh │ └── tsebra.sh ├── 5.ORTHOFINDER ### Ortholog gene phylogeny and gain/loss analysis ### │ └── orthofinder.sh ├── 6.MACRO_MICRO ### Macro- and micro-chromosome gene number analysis After creating 1 file per chromosome we print the gene number and size statistics using agat. ### │ ├── extract_per_chrom_gene_stats.sh │ └── plot_macromicro_stats.R ├── 7.PSMC ### PSMC analysis ### │ ├── 06.psmc.smk │ ├── 06.SGE_psmc.sh │ └── psmc_strura.R ├── 8.SNP_CALL ### SNP calling using assembled genome as reference and Illumina reads of passages. We also use do SNP calling using the HiFi reads ### │ ├── config │ │ └── config.yaml │ ├── envs │ ├── gatk_vcf_analysis_FINAL.R [...] │ ├── makefiles │ │ ├── 1.snp_calling_all.smk │ │ ├── gatk.smk │ │ ├── mapping.smk │ │ ├── preprocess.smk │ │ └── variant_recalibration.smk │ └── SGE_READQC.sh ├── ROHS │ ├── extract_bams.sh │ ├── ExtractTheta.sh │ ├── index_bams.sh │ └── ROHan.sh └── tree.tsv