NAME¶

last-dotplot - make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format

SYNOPSIS¶

last-dotplot --help last-dotplot [ options] maf-or-tab-alignments dotplot.png last-dotplot [ options] maf-or-tab-alignments dotplot.gif ...

DESCRIPTION¶

Draw a dotplot of pair-wise sequence alignments in MAF or tabular format.

OPTIONS¶

-h, --help

show this help message and exit

-1 PATTERN, --seq1=PATTERN

which sequences to show from the 1st genome

-2 PATTERN, --seq2=PATTERN

which sequences to show from the 2nd genome

-x WIDTH, --width=WIDTH

maximum width in pixels (default: 1000)

-y HEIGHT, --height=HEIGHT

maximum height in pixels (default: 1000)

-f FILE, --fontfile=FILE

TrueType or OpenType font file

-s SIZE, --fontsize=SIZE

TrueType or OpenType font size (default: 11)

-c COLOR, --forwardcolor=COLOR

color for forward alignments (default: red)

-r COLOR, --reversecolor=COLOR

color for reverse alignments (default: blue)

Unsequenced gap options:

--gap1=FILE

read genome1 unsequenced gaps from agp or gap file

--gap2=FILE

read genome2 unsequenced gaps from agp or gap file

--bridged-color=COLOR

color for bridged gaps (default: yellow)

--unbridged-color=COLOR

color for unbridged gaps (default: pink)