Diadema antillarum purge_dups output files and --dual-scaf assembly files

Note that the filename ragtag.HiFi.polished.simplified.filtered.fa.gz is the same file as the RefSeq assembly file available on NCBI with the assession number GCA_040938485.1. The filenames ragtag.HiFi.polished.simplified.hap.fa.gz and ragtag.HiFi.polished.simplified.purged.fa.gz are the output files after running Purge_Dups (v1.2.5) on the file ragtag.HiFi.polished.simplified.filtered.fa.gz. The filenames D02_Sp_assembly_dual_scaf_2025.bp.p_ctg.fa.gz, D02_Sp_assembly_dual_scaf_2025.bp.hap1.p_ctg.fa.gz, and D02_Sp_assembly_dual_scaf_2025.bp.hap2.p_ctg.fa.gz refer to the output files after running hifiasm -t 48 -o "${OUTPREFIX}" --dual-scaf "${IN}" on the adapter free HiFi reads deposited on NCBI under the accession number SRR32365430. The filename D02_Sp_assembly_dual_scaf_2025.bp.p_ctg_racon2_polished.fa.gz refers to the output file after racon polishing of Illumina DNA sequences of D02_Sp_assembly_dual_scaf_2025.bp.p_ctg.fa Below is the pipeline racon -t 32 D02_Sp_illumina_combined_trimmed_reads.fastq.gz D02_Sp_assembly_dual_scaf_map_Illum.sam D02_Sp_assembly_dual_scaf_2025.bp.p_ctg.fa > D02_Sp_assembly_dual_scaf_2025.bp.p_ctg_racon_polished.fa Round 2 (optional but common): minimap2 -t 32 -ax sr \ D02_Sp_assembly_dual_scaf_2025.bp.p_ctg_racon_polished.fa D02_Sp_illumina_combined_trimmed_reads.fastq.gz | samtools sort -@ 8 -O SAM -o D02_Sp_assembly_dual_scaf_2025.bp.p_ctg_racon_polished_mapped.sam racon -t 32 \ D02_Sp_illumina_combined_trimmed_reads.fastq.gz \ D02_Sp_assembly_dual_scaf_2025.bp.p_ctg_racon_polished_mapped.sam \ D02_Sp_assembly_dual_scaf_2025.bp.p_ctg_racon_polished.fa \ >D02_Sp_assembly_dual_scaf_2025.bp.p_ctg_racon2_polished.fa