Module extender 

Contig Extender Module

Provides k-mer based contig extension using paired-end reads. Extends assembled contigs by finding overlapping reads at contig edges.

Extension Modes

• Strict mode: High coverage requirement, low branching tolerance. Use for high-confidence extensions where accuracy is critical. Parameters: min_coverage=3, branching_threshold=0.1, max_n_ratio=0.02

• Relaxed mode: Lower coverage, higher branching tolerance. Use for unresolved cases where longer extensions are needed. Parameters: min_coverage=2, branching_threshold=0.2, max_n_ratio=0.05

Algorithm Overview

1. Build k-mer index from contig edges
2. Scan reads for matching k-mers
3. Collect extension candidates from overlapping reads
4. Build consensus sequence with branching detection
5. Repeat until no further extension possible

Structs

ContigExtender

K-mer based contig extender using paired-end reads.

ExtendedContig

Result of extension for a single contig.

ExtenderConfig

Configuration parameters for contig extension.

Functions

write_extended_contigs

Writes extended contigs to a FASTA file.