Manual

CLI help

# Get help in the command line
plot_nucmer --help

Required

Arguments	Required	Default value	Description
--subject	Y	NA	Path to FASTA file to be used as subject in alignment.
--sprefix	Y	NA	Prefix (name) to be used for subject FASTA. If prefix has a space it must be double quoted.
--query	Y	NA	Path to FASTA file to be used as query in alignment.
--qprefix	Y	NA	Prefix (name) to be used for query FASTA. If prefix has a space it must be double quoted.

Optinal customisation

Arguments	Required	Default value	Description
--out	N	plot_nucmer_${QUERY_PREFIX}_vs_${SUBJECT_PREFIX}	Prefix for nucmer plot outputs.
--scolor	N	gray70	R color for subject contigs.
--qcolor	N	steelblue	R color for query contigs.
--minlen	N	1000	Min. alignment length to be considered for plot.
--minid	N	90	Min. alignment identity to be considered for plot.

For a better understanding see the Quickstart.