flowchart TD
  0["Input dataset"];
  1["Input dataset"];
  2["Input dataset"];
  3["Input dataset collection"];
  4["GFA to FASTA"];
  5["GFA to FASTA"];
  6["Cutadapt"];
  7["Busco"];
  8["Busco"];
  9["Purge overlaps"];
  10["Collapse Collection"];
  11["Meryl"];
  12["Map with minimap2"];
  13["Quast"];
  14["Map with minimap2"];
  15["Meryl"];
  16["Purge overlaps"];
  17["Meryl"];
  18["Merqury"];
  19["Purge overlaps"];
  20["GenomeScope"];
  21["Purge overlaps"];
  22["Replace"];
  23["Compute"];
  24["Bionano Hybrid Scaffold"];
  25["Concatenate datasets"];
  26["Busco"];
  27["Replace"];
  28["Compute"];
  29["Concatenate datasets"];
  30["Purge overlaps"];
  31["Map with minimap2"];
  32["Search in textfiles"];
  33["Advanced Cut"];
  34["Advanced Cut"];
  35["BWA-MEM2"];
  36["BWA-MEM2"];
  37["Replace"];
  38["Quast"];
  39["Busco"];
  40["Map with minimap2"];
  41["Purge overlaps"];
  42["Convert"];
  43["Filter and merge"];
  44["Purge overlaps"];
  45["Advanced Cut"];
  46["bedtools BAM to BED"];
  47["PretextMap"];
  48["Purge overlaps"];
  49["Sort"];
  50["Pretext Snapshot"];
  51["Busco"];
  52["Quast"];
  53["SALSA"];
  54["BWA-MEM2"];
  55["BWA-MEM2"];
  56["Busco"];
  57["Quast"];
  58["Filter and merge"];
  59["PretextMap"];
  60["Pretext Snapshot"];
  3 -->|output| 6;
  4 -->|out_fa| 7;
  5 -->|out_fa| 8;
  5 -->|out_fa| 9;
  6 -->|out1| 10;
  6 -->|out1| 11;
  6 -->|out1| 12;
  5 -->|out_fa| 12;
  5 -->|out_fa| 13;
  4 -->|out_fa| 13;
  6 -->|out1| 13;
  9 -->|split_fasta| 14;
  9 -->|split_fasta| 14;
  11 -->|read_db| 15;
  12 -->|alignment_output| 16;
  15 -->|read_db| 17;
  5 -->|out_fa| 18;
  4 -->|out_fa| 18;
  15 -->|read_db| 18;
  16 -->|pbcstat_cov| 19;
  16 -->|calcuts_cutoff| 19;
  14 -->|alignment_output| 19;
  17 -->|read_db_hist| 20;
  19 -->|purge_dups_bed| 21;
  5 -->|out_fa| 21;
  20 -->|summary| 22;
  20 -->|model_params| 23;
  0 -->|output| 24;
  21 -->|get_seqs_purged| 24;
  21 -->|get_seqs_hap| 25;
  4 -->|out_fa| 25;
  21 -->|get_seqs_purged| 26;
  22 -->|outfile| 27;
  23 -->|out_file1| 28;
  24 -->|ngs_contigs_scaffold_trimmed| 29;
  24 -->|ngs_contigs_not_scaffolded_trimmed| 29;
  25 -->|out_file1| 30;
  10 -->|output| 31;
  25 -->|out_file1| 31;
  27 -->|outfile| 32;
  28 -->|out_file1| 33;
  28 -->|out_file1| 34;
  1 -->|output| 35;
  29 -->|out_file1| 35;
  2 -->|output| 36;
  29 -->|out_file1| 36;
  29 -->|out_file1| 37;
  29 -->|out_file1| 38;
  10 -->|output| 38;
  29 -->|out_file1| 39;
  30 -->|split_fasta| 40;
  30 -->|split_fasta| 40;
  31 -->|alignment_output| 41;
  32 -->|output| 42;
  36 -->|bam_output| 43;
  35 -->|bam_output| 43;
  41 -->|pbcstat_cov| 44;
  41 -->|calcuts_cutoff| 44;
  40 -->|alignment_output| 44;
  42 -->|out_file1| 45;
  43 -->|outfile| 46;
  43 -->|outfile| 47;
  44 -->|purge_dups_bed| 48;
  25 -->|out_file1| 48;
  46 -->|output| 49;
  47 -->|pretext_map_out| 50;
  48 -->|get_seqs_purged| 51;
  21 -->|get_seqs_purged| 52;
  48 -->|get_seqs_purged| 52;
  10 -->|output| 52;
  49 -->|out_file1| 53;
  37 -->|outfile| 53;
  1 -->|output| 54;
  53 -->|scaffolds_fasta| 54;
  2 -->|output| 55;
  53 -->|scaffolds_fasta| 55;
  53 -->|scaffolds_fasta| 56;
  53 -->|scaffolds_fasta| 57;
  10 -->|output| 57;
  55 -->|bam_output| 58;
  54 -->|bam_output| 58;
  58 -->|outfile| 59;
  59 -->|pretext_map_out| 60;