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44 lines
2.8 KiB
Markdown
44 lines
2.8 KiB
Markdown
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# Semantic Description of `obingslibrary` Package
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The `obingslibrary` package provides core functionality for **multiplexed high-throughput sequencing (HTS) data processing**, specifically designed to extract, validate, and assign biological samples from NGS reads using **dual-indexed barcodes** flanked by primers.
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## Key Functionalities
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1. **Primer & Tag Matching Structures**
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- `PrimerMatch`: Encodes location, orientation (`Forward`), mismatch count, and marker identity of primer hits.
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- `TagMatcher`: Functional interface for extracting sample-specific tags from sequence regions.
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2. **Distance Metrics**
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- `Hamming`: Counts character mismatches between equal-length strings (for strict mismatch tolerance).
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- `Levenshtein`: Computes edit distance allowing insertions/deletions (for indel-tolerant matching).
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3. **Tag Extraction Strategies**
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- `lookForTag`: Extracts delimited tags (e.g., between two identical delimiters).
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- `lookForRescueTag`: Robustly extracts tags despite indels or variable delimiter lengths.
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- `*Fixed/Delimited/RescueTagExtractor` methods: Support three tag formats per primer direction (fixed-length, delimited with exact delimiters, or rescue-tolerant).
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4. **Marker & Library Abstraction**
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- `NGSLibrary`: Holds a map of primer pairs (`PrimerPair`) to `Marker` objects.
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- Each `Marker`: Defines forward/reverse primer sequences, tag specifications (length/spacer/delimiter/indels), and sample-to-tag mappings.
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5. **Tag Assignment & Sample Identification**
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- `TagExtractor`: Extracts forward/reverse tags from primer-flanked regions and annotates them.
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- `SampleIdentifier`: Matches extracted tags to known samples using configurable matching modes:
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- `"strict"`: Exact match only.
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- `"hamming"`: Closest tag by Hamming distance (substitutions).
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- `"indel"`: Closest tag by Levenshtein distance.
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- Annotates results with matching mode, distances, and proposed tags.
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6. **Multi-Barcode Extraction**
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- `ExtractMultiBarcode`: Scans a full sequence for primer pairs (forward/reverse + their complements), detects valid amplicon intervals, and:
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- Extracts the internal barcode region.
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- Assigns tags → sample via `SampleIdentifier`.
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- Annotates each barcode with primer matches, errors, directionality.
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- Handles both orientations (`forward` and `reverse`) of the amplicon.
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7. **Parallel Processing Integration**
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- `ExtractMultiBarcodeSliceWorker`: Returns a reusable worker function for batch processing sequences, supporting options like indel tolerance and mismatch limits.
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## Use Case
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This package enables **demultiplexing** of NGS reads in amplicon-based workflows (e.g., metabarcoding), where samples are labeled with unique dual barcodes. It ensures robustness against sequencing errors and supports flexible tag design.
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