diff --git a/.codeboarding/Data_Configuration_Management.md b/.codeboarding/Data_Configuration_Management.md
new file mode 100644
index 0000000..ab38d51
--- /dev/null
+++ b/.codeboarding/Data_Configuration_Management.md
@@ -0,0 +1,65 @@
+```mermaid
+
+graph LR
+
+ Data_Configuration_Management["Data & Configuration Management"]
+
+ Data_Configuration_Management -- "configures" --> Main_Entry_Point_Orchestrator
+
+ Data_Configuration_Management -- "provides configuration to" --> Quality_Control_Alignment_Metrics
+
+ Data_Configuration_Management -- "provides reference data to" --> Sequence_Alignment_Modules
+
+ Data_Configuration_Management -- "provides reference data/configuration to" --> Variant_Analysis_Typing_Logic
+
+ click Data_Configuration_Management href "https://github.com/pfizer-opensource/LISTT/blob/main/.codeboarding//Data_Configuration_Management.md" "Details"
+
+```
+
+
+
+[](https://github.com/CodeBoarding/GeneratedOnBoardings)[](https://www.codeboarding.org/demo)[](mailto:contact@codeboarding.org)
+
+
+
+## Details
+
+
+
+These components and their relationships highlight a clear data-centric architecture where configuration and reference data are centrally managed and then distributed to the modules that consume them, ensuring consistency and proper execution across the pipeline.
+
+
+
+### Data & Configuration Management [[Expand]](./Data_Configuration_Management.md)
+
+This component is responsible for parsing command-line arguments, managing input/output file paths, and providing access to static configuration parameters (e.g., quality thresholds, reference lengths) and essential reference sequences/databases. It acts as the initial setup and data provisioning layer for the entire bioinformatics pipeline.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `src/cmd_parse.py` (1:1)
+
+- `variants/min_cov_metrics.csv` (1:1)
+
+- `variants/thresholds.csv` (1:1)
+
+- `variants/reference_lengths.csv` (1:1)
+
+- `alleles/ref_alleles.fasta` (1:1)
+
+- `ref/ospA_allele_fasta` (1:1)
+
+
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)
\ No newline at end of file
diff --git a/.codeboarding/Pipeline_Orchestrator.md b/.codeboarding/Pipeline_Orchestrator.md
new file mode 100644
index 0000000..7e2df3e
--- /dev/null
+++ b/.codeboarding/Pipeline_Orchestrator.md
@@ -0,0 +1,223 @@
+```mermaid
+
+graph LR
+
+ Pipeline_Orchestrator["Pipeline Orchestrator"]
+
+ Command_Line_Argument_Parser["Command-Line Argument Parser"]
+
+ Sequence_Aligner_OspA_Specific_["Sequence Aligner (OspA Specific)"]
+
+ BLAST_Aligner["BLAST Aligner"]
+
+ Alignment_Quality_Extractor["Alignment Quality Extractor"]
+
+ Best_Alignment_Selector["Best Alignment Selector"]
+
+ Alignment_QC_Checker["Alignment QC Checker"]
+
+ Consensus_Sequence_Builder["Consensus Sequence Builder"]
+
+ Variant_Similarity_Analyzer["Variant Similarity Analyzer"]
+
+ Pipeline_Orchestrator -- "receives configuration from" --> Command_Line_Argument_Parser
+
+ Pipeline_Orchestrator -- "initiates alignment" --> Sequence_Aligner_OspA_Specific_
+
+ Pipeline_Orchestrator -- "initiates alignment" --> BLAST_Aligner
+
+ Pipeline_Orchestrator -- "requests quality extraction" --> Alignment_Quality_Extractor
+
+ Pipeline_Orchestrator -- "queries for best alignment" --> Best_Alignment_Selector
+
+ Pipeline_Orchestrator -- "requests QC check" --> Alignment_QC_Checker
+
+ Pipeline_Orchestrator -- "initiates consensus building" --> Consensus_Sequence_Builder
+
+ Pipeline_Orchestrator -- "requests variant analysis" --> Variant_Similarity_Analyzer
+
+ click Pipeline_Orchestrator href "https://github.com/pfizer-opensource/LISTT/blob/main/.codeboarding//Pipeline_Orchestrator.md" "Details"
+
+```
+
+
+
+[](https://github.com/CodeBoarding/GeneratedOnBoardings)[](https://www.codeboarding.org/demo)[](mailto:contact@codeboarding.org)
+
+
+
+## Details
+
+
+
+The Pipeline Orchestrator is the central control unit of the bioinformatics pipeline, managing the overall execution flow based on the input mode (NGS or Assembly). It coordinates various stages by invoking specialized modules for specific tasks, ensuring a proper sequence of operations from initial data processing to final analysis.
+
+
+
+### Pipeline Orchestrator [[Expand]](./Pipeline_Orchestrator.md)
+
+The main entry point and coordinator of the entire bioinformatics pipeline. It directs the flow, handles file system setup (e.g., creating output directories), and orchestrates calls to other modules based on the input data type (NGS reads or assembled genomes).
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `Pipeline Orchestrator` (1:1)
+
+
+
+
+
+### Command-Line Argument Parser
+
+Responsible for parsing and validating command-line arguments provided by the user, configuring the pipeline's execution parameters and input files.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `Command-Line Argument Parser` (1:1)
+
+
+
+
+
+### Sequence Aligner (OspA Specific)
+
+Performs sequence alignment of raw reads against reference sequences, specifically tailored for OspA gene analysis in NGS mode. It generates alignment files (e.g., BAM, VCF).
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `Sequence Aligner (OspA Specific)` (1:1)
+
+
+
+
+
+### BLAST Aligner
+
+Utilizes the BLAST algorithm to align assembled genomes or sequences against a reference database, primarily used in the assembly mode of the pipeline.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `BLAST Aligner` (1:1)
+
+
+
+
+
+### Alignment Quality Extractor
+
+Extracts and processes quality metrics from variant call format (VCF) files generated during the alignment stage, providing data for downstream quality control.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `Alignment Quality Extractor` (1:1)
+
+
+
+
+
+### Best Alignment Selector
+
+Analyzes multiple alignment results and determines the optimal alignment based on predefined quality criteria, ensuring the most reliable data is used for subsequent steps.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `Best Alignment Selector` (1:1)
+
+
+
+
+
+### Alignment QC Checker
+
+Performs quality control checks on the selected best alignment, evaluating metrics such as coverage to ensure the alignment meets the required quality thresholds for further analysis.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `Alignment QC Checker` (1:1)
+
+
+
+
+
+### Consensus Sequence Builder
+
+Constructs a consensus sequence from the aligned reads or assembled genome, incorporating variant information to generate a representative sequence.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `Consensus Sequence Builder` (1:1)
+
+
+
+
+
+### Variant Similarity Analyzer
+
+Compares the generated consensus sequence against known variants or reference sequences to determine serotype, species, or other relevant genetic characteristics.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `Variant Similarity Analyzer` (1:1)
+
+
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)
\ No newline at end of file
diff --git a/.codeboarding/Post_Alignment_Processing_Quality_Control.md b/.codeboarding/Post_Alignment_Processing_Quality_Control.md
new file mode 100644
index 0000000..2e684b3
--- /dev/null
+++ b/.codeboarding/Post_Alignment_Processing_Quality_Control.md
@@ -0,0 +1,135 @@
+```mermaid
+
+graph LR
+
+ Consensus_Sequence_Builder["Consensus Sequence Builder"]
+
+ Alignment_Metrics_Calculator["Alignment Metrics Calculator"]
+
+ Alignment_Quality_Control_QC_Processor["Alignment Quality Control (QC) Processor"]
+
+ Quality_Score_Extractor["Quality Score Extractor"]
+
+ Sequence_Alignment_Module -- "produces aligned data for" --> Alignment_Metrics_Calculator
+
+ Sequence_Alignment_Module -- "provides aligned data with quality scores to" --> Quality_Score_Extractor
+
+ Alignment_Metrics_Calculator -- "generates metrics for" --> Alignment_Quality_Control_QC_Processor
+
+ Quality_Score_Extractor -- "provides quality scores to" --> Alignment_Quality_Control_QC_Processor
+
+ Alignment_Quality_Control_QC_Processor -- "provides quality-controlled data to" --> Consensus_Sequence_Builder
+
+ Consensus_Sequence_Builder -- "generates consensus sequences for" --> Downstream_Analysis_Components
+
+ Alignment_Quality_Control_QC_Processor -- "outputs filtered data/reports to" --> Downstream_Analysis_Components
+
+ Main_Pipeline_Orchestrator -- "orchestrates" --> Consensus_Sequence_Builder
+
+ Consensus_Sequence_Builder -- "is orchestrated by" --> Main_Pipeline_Orchestrator
+
+ Main_Pipeline_Orchestrator -- "orchestrates" --> Alignment_Metrics_Calculator
+
+ Alignment_Metrics_Calculator -- "is orchestrated by" --> Main_Pipeline_Orchestrator
+
+ Main_Pipeline_Orchestrator -- "orchestrates" --> Alignment_Quality_Control_QC_Processor
+
+ Alignment_Quality_Control_QC_Processor -- "is orchestrated by" --> Main_Pipeline_Orchestrator
+
+ Main_Pipeline_Orchestrator -- "orchestrates" --> Quality_Score_Extractor
+
+ Quality_Score_Extractor -- "is orchestrated by" --> Main_Pipeline_Orchestrator
+
+```
+
+
+
+[](https://github.com/CodeBoarding/GeneratedOnBoardings)[](https://www.codeboarding.org/demo)[](mailto:contact@codeboarding.org)
+
+
+
+## Details
+
+
+
+The `Post-Alignment Processing & Quality Control` component is a crucial stage in the bioinformatics pipeline, focusing on refining and validating aligned sequencing data. It ensures the accuracy and reliability of the data before downstream analyses.
+
+
+
+### Consensus Sequence Builder
+
+This component is responsible for constructing high-quality consensus sequences from aligned reads. It likely involves algorithms to resolve discrepancies, handle indels, and determine the most probable base at each position, resulting in a single, representative sequence.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `Consensus Sequence Builder`
+
+
+
+
+
+### Alignment Metrics Calculator
+
+This component calculates various metrics to assess the quality and characteristics of the alignments. This includes metrics such as read counts, coverage depth, mapping quality, and potentially error rates. These metrics are vital for evaluating the success of the alignment process and identifying potential issues.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `Alignment Metrics Calculator`
+
+
+
+
+
+### Alignment Quality Control (QC) Processor
+
+This component performs overall quality control on the aligned data. It likely integrates the metrics calculated by the `Alignment Metrics Calculator` and applies predefined criteria to filter, flag, or select the "best" alignments. This could involve removing low-quality alignments, identifying regions of low coverage, or ensuring data meets specific thresholds.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `Alignment Quality Control (QC) Processor`
+
+
+
+
+
+### Quality Score Extractor
+
+This component is specifically designed to extract and potentially process quality scores associated with sequencing reads or aligned bases. Quality scores are crucial for assessing the confidence of base calls and are often used in conjunction with alignment metrics for more nuanced quality control.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `Quality Score Extractor`
+
+
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)
\ No newline at end of file
diff --git a/.codeboarding/Sequence_Alignment_Pre_processing.md b/.codeboarding/Sequence_Alignment_Pre_processing.md
new file mode 100644
index 0000000..87f8ca0
--- /dev/null
+++ b/.codeboarding/Sequence_Alignment_Pre_processing.md
@@ -0,0 +1,127 @@
+```mermaid
+
+graph LR
+
+ Main_Pipeline_Orchestrator["Main Pipeline Orchestrator"]
+
+ Sequence_Alignment_Pre_processing["Sequence Alignment & Pre-processing"]
+
+ Consensus_Sequence_Builder["Consensus Sequence Builder"]
+
+ Quality_Control_Alignment_Metrics["Quality Control & Alignment Metrics"]
+
+ Main_Pipeline_Orchestrator -- "initiates" --> Sequence_Alignment_Pre_processing
+
+ Sequence_Alignment_Pre_processing -- "outputs to" --> Consensus_Sequence_Builder
+
+ Sequence_Alignment_Pre_processing -- "outputs to" --> Quality_Control_Alignment_Metrics
+
+ Main_Pipeline_Orchestrator -- "initiates" --> Consensus_Sequence_Builder
+
+ Main_Pipeline_Orchestrator -- "initiates" --> Quality_Control_Alignment_Metrics
+
+ click Sequence_Alignment_Pre_processing href "https://github.com/pfizer-opensource/LISTT/blob/main/.codeboarding//Sequence_Alignment_Pre_processing.md" "Details"
+
+```
+
+
+
+[](https://github.com/CodeBoarding/GeneratedOnBoardings)[](https://www.codeboarding.org/demo)[](mailto:contact@codeboarding.org)
+
+
+
+## Details
+
+
+
+One paragraph explaining the functionality which is represented by this graph. What the main flow is and what is its purpose.
+
+
+
+### Main Pipeline Orchestrator
+
+This component serves as the central control unit for the entire bioinformatics pipeline. It is responsible for parsing command-line arguments, coordinating the execution of various pipeline stages, and managing the overall workflow. It acts as the entry point for the application.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `run_pipe` (1:1)
+
+- `cmd_parse` (1:1)
+
+
+
+
+
+### Sequence Alignment & Pre-processing [[Expand]](./Sequence_Alignment_Pre_processing.md)
+
+This component handles the initial processing of raw sequence data. It performs sequence alignment against reference genomes or databases, generating alignment files (e.g., BAM/SAM). It supports both NGS and Assembly modes, preparing data for downstream analysis.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `align_to_refs` (1:1)
+
+- `blast_align` (1:1)
+
+- `ospA_aligner` (1:1)
+
+
+
+
+
+### Consensus Sequence Builder
+
+This component is responsible for constructing consensus sequences from aligned sequence data. After reads are aligned to a reference, this component aggregates the aligned information to derive a single, representative sequence for each region.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `build_consensus` (1:1)
+
+
+
+
+
+### Quality Control & Alignment Metrics
+
+This component performs quality control checks on the aligned sequence data and generates various metrics to assess the quality of alignments. This helps in identifying potential issues with sequencing data or alignment process.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `alignment_metrics` (1:1)
+
+- `pull_qual` (1:1)
+
+- `qc_alignments` (1:1)
+
+
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)
\ No newline at end of file
diff --git a/.codeboarding/Variant_Analysis_Typing.md b/.codeboarding/Variant_Analysis_Typing.md
new file mode 100644
index 0000000..d55fa38
--- /dev/null
+++ b/.codeboarding/Variant_Analysis_Typing.md
@@ -0,0 +1,215 @@
+```mermaid
+
+graph LR
+
+ Consensus_Sequence_Builder["Consensus Sequence Builder"]
+
+ Variant_Analysis_Typing_Orchestrator["Variant Analysis & Typing Orchestrator"]
+
+ Reference_Data_Manager["Reference Data Manager"]
+
+ Sequence_Comparison_Alignment_Engine["Sequence Comparison & Alignment Engine"]
+
+ Typing_Interpretation_Logic["Typing & Interpretation Logic"]
+
+ Analysis_Report_Generator["Analysis Report Generator"]
+
+ Main_Entry_Point_Orchestrator["Main Entry Point/Orchestrator"]
+
+ External_Tools["External Tools"]
+
+ Analysis_Reports["Analysis Reports"]
+
+ Main_Entry_Point_Orchestrator -- "initiates" --> Variant_Analysis_Typing_Orchestrator
+
+ Consensus_Sequence_Builder -- "provides input to" --> Reference_Data_Manager
+
+ Variant_Analysis_Typing_Orchestrator -- "directs to load data" --> Reference_Data_Manager
+
+ Variant_Analysis_Typing_Orchestrator -- "triggers" --> Sequence_Comparison_Alignment_Engine
+
+ Sequence_Comparison_Alignment_Engine -- "utilizes" --> External_Tools
+
+ Variant_Analysis_Typing_Orchestrator -- "passes results to" --> Typing_Interpretation_Logic
+
+ Typing_Interpretation_Logic -- "provides interpreted data to" --> Analysis_Report_Generator
+
+ Variant_Analysis_Typing_Orchestrator -- "instructs to create reports" --> Analysis_Report_Generator
+
+ Analysis_Report_Generator -- "produces" --> Analysis_Reports
+
+```
+
+
+
+[](https://github.com/CodeBoarding/GeneratedOnBoardings)[](https://www.codeboarding.org/demo)[](mailto:contact@codeboarding.org)
+
+
+
+## Details
+
+
+
+One paragraph explaining the functionality which is represented by this graph. What the main flow is and what is its purpose.
+
+
+
+### Consensus Sequence Builder
+
+This component is responsible for generating the consensus sequence from raw sequencing reads. It processes the input sequencing data to produce a high-quality consensus sequence, which then serves as the primary query input for the downstream variant analysis and typing pipeline.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `src.build_consensus`
+
+
+
+
+
+### Variant Analysis & Typing Orchestrator
+
+This is the central control component for the entire variant analysis and typing stage, primarily embodied by the `VariantSimilarity` class. It orchestrates the workflow, coordinating the loading of input data and references, initiating sequence comparisons and alignments, processing results (including variant and serotype determination), and triggering report generation. It ensures the seamless execution of all sub-tasks within this pipeline segment.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `src.align_to_refs.VariantSimilarity` (18:152)
+
+- `src.align_to_refs.VariantSimilarity.run` (127:152)
+
+
+
+
+
+### Reference Data Manager
+
+Responsible for handling the input query consensus sequence and loading the comprehensive database of known reference variants along with their associated serotypes. This component ensures that all necessary comparative data is correctly loaded, parsed, and made available for the downstream analysis.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `src.align_to_refs.VariantSimilarity.load_query` (34:44)
+
+- `src.align_to_refs.VariantSimilarity.load_refs` (46:51)
+
+- `src.align_to_refs.VariantSimilarity.import_serotypes` (53:58)
+
+
+
+
+
+### Sequence Comparison & Alignment Engine
+
+This component performs the core computational task of comparing the query sequence against the reference sequences. It first attempts a rapid direct match. If no direct match is found, it orchestrates the execution of external multiple sequence alignment tools (e.g., MAFFT) to align the sequences and subsequently calculates sequence identity scores from these alignments.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `src.align_to_refs.VariantSimilarity.calc_identity` (60:64)
+
+- `src.align_to_refs.VariantSimilarity.run_mafft` (75:90)
+
+- `src.align_to_refs.VariantSimilarity.align_seqs` (93:114)
+
+
+
+
+
+### Typing & Interpretation Logic
+
+This component encapsulates the specific business logic to interpret the results from the sequence comparison and alignment. It determines the closest known variant based on the calculated identity scores and assigns the corresponding serotype and species. This logic is integrated within the `VariantSimilarity.run` method, where computational results are translated into meaningful biological conclusions.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `src.align_to_refs.VariantSimilarity.run` (127:152)
+
+
+
+
+
+### Analysis Report Generator
+
+Responsible for compiling, formatting, and writing the final output report. This report summarizes the variant analysis results, including the identified variant, its similarity to reference sequences, and the assigned typing information, making the findings accessible to the user.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `src.align_to_refs.VariantSimilarity.write_report` (116:125)
+
+
+
+
+
+### Main Entry Point/Orchestrator
+
+Represents the main entry point or orchestrator of the system.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### External Tools
+
+Represents external tools utilized by the system.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### Analysis Reports
+
+Represents the final analysis reports generated by the system.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)
\ No newline at end of file
diff --git a/.codeboarding/on_boarding.md b/.codeboarding/on_boarding.md
new file mode 100644
index 0000000..5d01454
--- /dev/null
+++ b/.codeboarding/on_boarding.md
@@ -0,0 +1,179 @@
+```mermaid
+
+graph LR
+
+ Pipeline_Orchestrator["Pipeline Orchestrator"]
+
+ Data_Configuration_Management["Data & Configuration Management"]
+
+ Sequence_Alignment_Pre_processing["Sequence Alignment & Pre-processing"]
+
+ Post_Alignment_Processing_Quality_Control["Post-Alignment Processing & Quality Control"]
+
+ Variant_Analysis_Typing["Variant Analysis & Typing"]
+
+ Pipeline_Orchestrator -- "Controls" --> Data_Configuration_Management
+
+ Pipeline_Orchestrator -- "Orchestrates" --> Sequence_Alignment_Pre_processing
+
+ Pipeline_Orchestrator -- "Orchestrates" --> Post_Alignment_Processing_Quality_Control
+
+ Pipeline_Orchestrator -- "Orchestrates" --> Variant_Analysis_Typing
+
+ Variant_Analysis_Typing -- "Outputs Typing Results To" --> Pipeline_Orchestrator
+
+ Data_Configuration_Management -- "Provides Configuration To" --> Pipeline_Orchestrator
+
+ Data_Configuration_Management -- "Supplies Reference Data To" --> Sequence_Alignment_Pre_processing
+
+ Data_Configuration_Management -- "Supplies Parameters To" --> Post_Alignment_Processing_Quality_Control
+
+ Data_Configuration_Management -- "Supplies Reference Alleles To" --> Variant_Analysis_Typing
+
+ Sequence_Alignment_Pre_processing -- "Generates Aligned Data For" --> Post_Alignment_Processing_Quality_Control
+
+ Sequence_Alignment_Pre_processing -- "Generates Raw Variants For" --> Variant_Analysis_Typing
+
+ Post_Alignment_Processing_Quality_Control -- "Produces Refined Data For" --> Variant_Analysis_Typing
+
+ Post_Alignment_Processing_Quality_Control -- "Provides Quality Metrics To" --> Pipeline_Orchestrator
+
+ click Pipeline_Orchestrator href "https://github.com/pfizer-opensource/LISTT/blob/main/.codeboarding//Pipeline_Orchestrator.md" "Details"
+
+ click Data_Configuration_Management href "https://github.com/pfizer-opensource/LISTT/blob/main/.codeboarding//Data_Configuration_Management.md" "Details"
+
+ click Sequence_Alignment_Pre_processing href "https://github.com/pfizer-opensource/LISTT/blob/main/.codeboarding//Sequence_Alignment_Pre_processing.md" "Details"
+
+ click Post_Alignment_Processing_Quality_Control href "https://github.com/pfizer-opensource/LISTT/blob/main/.codeboarding//Post_Alignment_Processing_Quality_Control.md" "Details"
+
+ click Variant_Analysis_Typing href "https://github.com/pfizer-opensource/LISTT/blob/main/.codeboarding//Variant_Analysis_Typing.md" "Details"
+
+```
+
+
+
+[](https://github.com/CodeBoarding/GeneratedOnBoardings)[](https://www.codeboarding.org/demo)[](mailto:contact@codeboarding.org)
+
+
+
+## Details
+
+
+
+High-level data flow overview of the LISTT bioinformatics pipeline. Project Type: Bioinformatics Pipeline. Architectural Patterns: Pipeline Architecture, Modular Design, Command-Line Interface (CLI) Application, Data-Centric Architecture, External Tool Orchestration.
+
+
+
+### Pipeline Orchestrator [[Expand]](./Pipeline_Orchestrator.md)
+
+The central control unit that manages the overall execution flow of the bioinformatics pipeline. It coordinates different stages based on the input mode (NGS or Assembly) and ensures proper sequencing of operations.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `src/run_pipe.py` (1:1)
+
+
+
+
+
+### Data & Configuration Management [[Expand]](./Data_Configuration_Management.md)
+
+Handles command-line argument parsing, loads various configuration parameters (e.g., quality thresholds, reference lengths), manages input/output paths, and provides access to all necessary reference sequences and pre-indexed databases.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `src/cmd_parse.py` (1:1)
+
+- `variants/min_cov_metrics.csv` (1:1)
+
+- `variants/thresholds.csv` (1:1)
+
+- `variants/reference_lengths.csv` (1:1)
+
+- `alleles/ref_alleles.fasta` (1:1)
+
+- `ref/ospA_allele_fasta` (1:1)
+
+
+
+
+
+### Sequence Alignment & Pre-processing [[Expand]](./Sequence_Alignment_Pre_processing.md)
+
+Performs the initial processing of raw sequence data. This includes aligning raw sequencing reads (for NGS mode) or assembled sequences (for Assembly mode) to specified reference genomes or curated databases, generating alignment files (e.g., BAM/SAM), and performing initial variant calling or sequence curation.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `src/ospA_aligner.py` (1:1)
+
+- `src/blast_align.py` (1:1)
+
+
+
+
+
+### Post-Alignment Processing & Quality Control [[Expand]](./Post_Alignment_Processing_Quality_Control.md)
+
+Refines and assesses the quality of aligned data. This component constructs high-quality consensus sequences from aligned reads or processed variant calls and evaluates alignment quality by calculating various metrics (e.g., read counts, coverage), selecting the "best" alignment based on predefined criteria.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `src/build_consensus.py` (1:1)
+
+- `src/alignment_metrics.py` (1:1)
+
+- `src/qc_alignments.py` (1:1)
+
+- `src/pull_qual.py` (1:1)
+
+
+
+
+
+### Variant Analysis & Typing [[Expand]](./Variant_Analysis_Typing.md)
+
+The final analytical stage of the pipeline. It analyzes genetic variants, compares query sequences or identified variants to known reference alleles, and performs typing or determines similarity based on these comparisons, generating the ultimate biological insights.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `src/align_to_refs.py` (1:1)
+
+
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)
\ No newline at end of file