Output file formats

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Lauren Coombe edited this page Oct 18, 2023 · 3 revisions

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)