Output file formats

ntLink output file formats

Path files

Suffix: .path

Format: tab-separated

• Column 1: Scaffold name
• Column 2: Space-separated description of scaffold composition. Consists of contig names with orientation (+ or -, ex. ctg1234+) and gap sizes (Ex. 20N)

Verbose mapping files

Suffix: .verbose_mapping.tsv

Format: tab-separated

• Column 1: Read name
• Column 2: Contig name
• Column 3: Number of mapping minimizers
• Column 4: Space-separated list of the mapping minimizers in format <contig_position>:<contig_strand>_<read_position>:<read_strand>

PAF mapping files

Suffix: .paf

Format: tab-separated

• Column 1: Query name
• Column 2: Query length
• Column 3: Query start (0-based)
• Column 4: Query end (0-based)
• Column 5: Strand ("+" or "-")
• Column 6: Target name
• Column 7: Target length
• Column 8: Target start (0-based)
• Column 9: Target end (0-based)
• Column 10: Number of minimizer mappings/matches
• Column 11: Mapping block length on contig
• Column 12: Always 255 (indicating missing mapping quality)