Graphical Representation of the Pipeline¶

flowchart TD %% Inputs subgraph Inputs illumina["Illumina Short Reads"] pacbio["PacBio Long Reads"] ont["ONT Long Reads"] ref_fasta["Reference FASTA"] mod_fasta["Modified FASTA"] end style Inputs fill:#E6F4EA,stroke:#2E7D32,stroke-width:2px %% Short-read pipeline subgraph ShortReadPipeline["Short-Read Pipeline"] illumina --> trimgalore["TrimGalore / QC"] trimgalore --> bwa_index["BWA Index"] bwa_index --> bwa_map["BWA Mapping"] bwa_map --> samtools_sort["Samtools Sort & Stats"] samtools_sort --> picard["Picard / MultiQC"] samtools_sort --> sr_vcf["VCF Output (Short-Read)"] sr_vcf --> short_mod["Optional: Compare to Modified"] short_mod --> agg_tbl end style ShortReadPipeline fill:#D0F0C0,stroke:#388E3C,stroke-width:2px %% Long-read PacBio pipeline subgraph LongReadPacBio["Long-Read PacBio Pipeline"] pacbio --> minimap2_pb["Minimap2 Mapping"] minimap2_pb --> samtools_sort_pb["Samtools Sort & Stats"] samtools_sort_pb --> pb_sv["SV Calling (CuteSV / Sniffles / Debreak)"] pb_sv --> pb_vcf["VCF Output (PacBio)"] pb_vcf --> long_mod_pb["Optional: Compare to Modified"] long_mod_pb --> agg_tbl end style LongReadPacBio fill:#D0F0C0,stroke:#388E3C,stroke-width:2px %% Long-read ONT pipeline subgraph LongReadONT["Long-Read ONT Pipeline"] ont --> minimap2_ont["Minimap2 Mapping"] minimap2_ont --> samtools_sort_ont["Samtools Sort & Stats"] samtools_sort_ont --> ont_sv["SV Calling (CuteSV / Sniffles / Debreak)"] ont_sv --> ont_vcf["VCF Output (ONT)"] ont_vcf --> long_mod_ont["Optional: Compare to Modified"] long_mod_ont --> agg_tbl end style LongReadONT fill:#D0F0C0,stroke:#388E3C,stroke-width:2px %% Reference vs Modified pipeline subgraph RefVsMod["Reference vs Modified Pipeline"] ref_fasta --> run_ref_x_mod_decision{"--run_ref_x_mod?"} mod_fasta --> run_ref_x_mod_decision run_ref_x_mod_decision -->|Yes| nucmer["NUCmer Alignment"] run_ref_x_mod_decision -->|No| skip_syri["Skip SYRI"] nucmer --> delta_filter["Delta Filter"] delta_filter --> show_coords["Show Coords"] show_coords --> syri_vcf["VCF Output (assemblysyri)"] syri_vcf --> agg_tbl end style RefVsMod fill:#D0F0C0,stroke:#388E3C,stroke-width:2px %% SV table aggregation (central) subgraph SVTable["SV Table Aggregation"] agg_tbl["Mix SV Tables"] --> restructure["Restructure SV Table (create_sv_output.py)"] end style SVTable fill:#FFF3E0,stroke:#F57C00,stroke-width:2px %% Truvari comparison (central) subgraph Truvari["Truvari Comparison (Conditional)"] sr_vcf --> truvari_in["VCFs for Truvari"] pb_vcf --> truvari_in ont_vcf --> truvari_in syri_vcf --> truvari_in truvari_in --> check_truvari{"--run_truvari?"} check_truvari -->|Yes| truvari["Compare SVs (Truvari)"] check_truvari -->|No| skip_truvari["Skip Truvari"] truvari --> final_report["Truvari Reports / Summary"] end style Truvari fill:#D0F0C0,stroke:#2E7D32,stroke-width:2px %% Central alignment restructure --> truvari_in