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The main output file from ntSynt-viz is the chromosome painting ribbon plot in PNG or PDF format. Here, we describe the other output files that ntSynt-viz will generate.

Descriptions of file formats

*renamed.sorted.blocks.tsv

Synteny blocks in the ntSynt format (https://github.com/bcgsc/ntsynt?tab=readme-ov-file#output-files)

• In the last ("reason") column, if a synteny block was reverse complemented due to chromosome strand normalization (if --normalize is supplied), this will be indicated by a _rev suffix

*links.tsv

File with coordinates for links that will be plotted as ribbons in the ribbon plots. Columns:

• block_id: synteny block ID
• seq_id: chromosome name of genome1
• bin_id: assembly name of genome1
• start: start coordinate of synteny block in genome1
• end: end coordinate of synteny block in genome1
• seq_id2: chromosome name of genome2
• bin_id2: assembly name of genome2
• start2: start coordinate of synteny block in genome2
• end2: end coordinate of synteny block in genome2
• strand: + if the synteny blocks are on the same strand, else -
• colour_block: The chromosome name in the target assembly that will be used for colouring the ribbon

*sequence_lengths.sorted.tsv

File with lengths of chromosomes of all compared genomes Columns:

• bin_id: assembly name
• seq_id: chromosome name
• length: length of chromosome (in bp)
• relative_orientation: if --normalize is invoked, "-" if the chromosome was reverse-complemented to be normalized to the target genome, else "+". If --normalize is not invoked, will always be "+"

*est-distances.tsv

If --tree is not specified, this file contains the estimated pairwise synteny-based distances between the genomes Columns:

• Genome 1
• Genome 2
• Estimated distance (value from 0-1)

*est-distances.phylip

If --tree is not specified, this file contains the same distance estimation information as the previous file, but in phylip format

*order.tsv

File lists the order that the genomes will be plotted in top-to-bottom in the chromosome painting ribbon plot

*chrom-paint-feats.tsv

File lists the start/end coordinates of each synteny block, providing all the information needed for the chromosome painting part of the plots Columns:

• Synteny block ID
• Chromosome ID
• Genome name
• Start coordinate of synteny block
• End coordinate of synteny block
• The name of the target chromosome that will be used for colouring this segment