mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-04-30 12:00:39 +00:00
Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
44 lines
2.8 KiB
Markdown
44 lines
2.8 KiB
Markdown
# Semantic Description of `obingslibrary` Package
|
|
|
|
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.
|
|
|
|
## Key Functionalities
|
|
|
|
1. **Primer & Tag Matching Structures**
|
|
- `PrimerMatch`: Encodes location, orientation (`Forward`), mismatch count, and marker identity of primer hits.
|
|
- `TagMatcher`: Functional interface for extracting sample-specific tags from sequence regions.
|
|
|
|
2. **Distance Metrics**
|
|
- `Hamming`: Counts character mismatches between equal-length strings (for strict mismatch tolerance).
|
|
- `Levenshtein`: Computes edit distance allowing insertions/deletions (for indel-tolerant matching).
|
|
|
|
3. **Tag Extraction Strategies**
|
|
- `lookForTag`: Extracts delimited tags (e.g., between two identical delimiters).
|
|
- `lookForRescueTag`: Robustly extracts tags despite indels or variable delimiter lengths.
|
|
- `*Fixed/Delimited/RescueTagExtractor` methods: Support three tag formats per primer direction (fixed-length, delimited with exact delimiters, or rescue-tolerant).
|
|
|
|
4. **Marker & Library Abstraction**
|
|
- `NGSLibrary`: Holds a map of primer pairs (`PrimerPair`) to `Marker` objects.
|
|
- Each `Marker`: Defines forward/reverse primer sequences, tag specifications (length/spacer/delimiter/indels), and sample-to-tag mappings.
|
|
|
|
5. **Tag Assignment & Sample Identification**
|
|
- `TagExtractor`: Extracts forward/reverse tags from primer-flanked regions and annotates them.
|
|
- `SampleIdentifier`: Matches extracted tags to known samples using configurable matching modes:
|
|
- `"strict"`: Exact match only.
|
|
- `"hamming"`: Closest tag by Hamming distance (substitutions).
|
|
- `"indel"`: Closest tag by Levenshtein distance.
|
|
- Annotates results with matching mode, distances, and proposed tags.
|
|
|
|
6. **Multi-Barcode Extraction**
|
|
- `ExtractMultiBarcode`: Scans a full sequence for primer pairs (forward/reverse + their complements), detects valid amplicon intervals, and:
|
|
- Extracts the internal barcode region.
|
|
- Assigns tags → sample via `SampleIdentifier`.
|
|
- Annotates each barcode with primer matches, errors, directionality.
|
|
- Handles both orientations (`forward` and `reverse`) of the amplicon.
|
|
|
|
7. **Parallel Processing Integration**
|
|
- `ExtractMultiBarcodeSliceWorker`: Returns a reusable worker function for batch processing sequences, supporting options like indel tolerance and mismatch limits.
|
|
|
|
## Use Case
|
|
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.
|