mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-04-30 12:00:39 +00:00
63 lines
3.5 KiB
Markdown
63 lines
3.5 KiB
Markdown
|
# `obipairing` Package — Functional Overview
|
||
|
|
|
||
|
|
The `obipairing` package enables robust merging of paired-end next-generation sequencing (NGS) reads within the OBITools4 ecosystem. It bridges input parsing, alignment configuration, and consensus assembly—supporting both high-accuracy overlap-based merging and lightweight fallback concatenation when overlaps are unreliable.
|
||
|
|
|
||
|
|
## Public API Summary
|
||
|
|
|
||
|
|
### CLI Interface (`obipairing/cli.go`)
|
||
|
|
- **Input specification**:
|
||
|
|
`--forward-reads` (`-F`) and `--reverse-reads` (`-R`) flags accept FASTQ/FASTA file paths.
|
||
|
|
- **Alignment tuning**:
|
||
|
|
- `_Delta` (`--delta`, default `5`) — buffer for refining initial overlap detection.
|
||
|
|
- `_MinOverlap` (`--min-overlap`, default `20`) — minimum overlap length.
|
||
|
|
- `_MinIdentity` (`--min-identity`, default `90`) — minimum % identity for valid alignment.
|
||
|
|
- `_GapPenalty` (`--gap-penalty`, default `2`) — gap cost multiplier vs mismatches.
|
||
|
|
- `_PenaltyScale` (`--scale`, default `1`) — global scoring scaling factor.
|
||
|
|
- **Alignment mode control**:
|
||
|
|
- Fast heuristic enabled by default; `--exact-mode` disables it.
|
||
|
|
- Absolute scoring in fast mode via `--fast-absolute`.
|
||
|
|
- **Output customization**:
|
||
|
|
`--without-stat` omits alignment statistics from consensus headers.
|
||
|
|
- Extends generic I/O options inherited from `obiconvert` for pipeline compatibility.
|
||
|
|
|
||
|
|
### Core Assembly Functions (`obipairing/assemble.go`)
|
||
|
|
- **`JoinPairedSequence(seqA, seqB *obiseq.BioSequence, inplace bool) (consensus *obiseq.BioSequence)`**
|
||
|
|
Concatenates forward and reverse reads with a `..........` (10-dot) separator.
|
||
|
|
- Quality scores for dots set to Phred `Q=0` if both inputs are quality-tracked.
|
||
|
|
- Supports in-place recycling (`inplace=true`) to reduce allocations.
|
||
|
|
|
||
|
|
- **`AssemblePESequences(...)`**
|
||
|
|
Performs high-fidelity paired-end assembly:
|
||
|
|
- Uses `obialign.PEAlign` with a two-stage process:
|
||
|
|
1. **Fast heuristic** (`FAST`) to locate candidate overlap region.
|
||
|
|
2. **Dynamic programming refinement**, extended by `_Delta`.
|
||
|
|
- Validates alignment against thresholds (`minOverlap`, `minIdentity`).
|
||
|
|
Falls back to join if criteria unmet.
|
||
|
|
- Optionally annotates output with alignment metadata:
|
||
|
|
```go
|
||
|
|
"mode" → "alignment" or "join"
|
||
|
|
"ali_length" → overlap length
|
||
|
|
"score_norm" → normalized alignment score
|
||
|
|
"identity" → % identity over overlap
|
||
|
|
"directionality"→ orientation (e.g., FR)
|
||
|
|
```
|
||
|
|
- Supports in-place reuse (`inplace`) and absolute/relative scoring via `fastModeRel`.
|
||
|
|
|
||
|
|
- **`IAssemblePESequencesBatch(...)`**
|
||
|
|
Parallelizes assembly over batches of read pairs:
|
||
|
|
- Consumes iterators from `PairWith` (e.g., via `obiiter`).
|
||
|
|
- Launches configurable workers (`nworkers`) and channel buffer size.
|
||
|
|
- Internally reverse-complements the second read before alignment (`seqB.ReverseComplement()`).
|
||
|
|
- Yields assembled consensus sequences via an iterator.
|
||
|
|
|
||
|
|
### Configuration & Parameter Access
|
||
|
|
- Getter functions (`CLI*`) expose parsed CLI parameters (e.g., `CLIMinOverlap()`, `CLIGapPenalty()`), enabling downstream alignment modules to reuse CLI-defined settings.
|
||
|
|
|
||
|
|
### Annotation Semantics
|
||
|
|
Each assembled sequence carries annotations describing the assembly mode and, when applicable:
|
||
|
|
- Alignment scores (`ali_score`, `score_norm`)
|
||
|
|
- Overlap metrics (`ali_length`, `identity`)
|
||
|
|
- Fast-mode metadata (e.g., `"pairing_fast_score"`) when heuristic alignment is used.
|
||
|
|
|
||
|
|
Designed for scalability, low memory footprint, and integration with `obiseq`, `obiiter`, and alignment backends in OBITools4.
|