kuva synteny

Synteny / genomic alignment ribbon plot.

Input: two files:

Sequences file (positional): TSV with sequence name and length columns.
Blocks file (--blocks-file): TSV with columns seq1, start1, end1, seq2, start2, end2, strand.

# sequences.tsv
name    length
Chr1A   2800000
Chr1B   2650000

# blocks.tsv
seq1   start1  end1    seq2   start2  end2    strand
Chr1A  56000   137237  Chr1B  63958   143705  +
Chr1A  150674  271188  Chr1B  165366  303075  -

Flag	Default	Description
`--blocks-file <FILE>`	(required)	Blocks TSV file
`--bar-height <PX>`	`18.0`	Sequence bar height in pixels
`--opacity <F>`	`0.65`	Block ribbon opacity
`--proportional`	off	Scale bar widths proportionally to sequence length
`--legend <LABEL>`	—	Show legend

kuva synteny synteny_seqs.tsv --blocks-file synteny_blocks.tsv

kuva synteny synteny_seqs.tsv --blocks-file synteny_blocks.tsv \
    --proportional --legend "synteny blocks"

See also: Shared flags — output, appearance, axes, log scale.