Manual

CLI help

# Get help in the command line
plot_circos --help

Input files

Arguments	Required	Default value	Description
--fofn	Y	NA	File of file names (CSV: fasta path,prefix,color) containing list of fastas to draw circos plot.
--labels	N	NA	TSV file containing the label definitions for plotting. The file must contain 4 or 5 columns as shown at http://circos.ca/documentation/tutorials/2d_tracks/text_1/lesson.
--tiles	N	NA	TSV file containing the tile definitions for plotting. The file must contain 3 or 4 columns as shown at http://circos.ca/documentation/tutorials/configuration/data_files.

Output files

Arguments	Required	Default value	Description
--outdir	N	./results	Path to output directory.

Workflow options

Arguments	Required	Default value	Description
--threads	N	1	Set the number of threads to be used by the software.
--minlen	N	10000	Min size of contigs to consider for plot.
--minid	N	85	Min. percentage id to filter the results of blastn to draw links.
--linklen	N	5000	Min. link (blastn hit) length to display in plot.
--show_intrachr	N	false	Tells the program to create a conf file showing intra chr links. Mandatory if using only one FASTA, otherwise, links will not be shown.
--gc_window	N	5000	GC skew window size.
--gc_step	N	5000	GC skew step size.

Helpful scripts

gff2labels

Activated with --gff2labels parameter.

Syntax: plot_circos [ --gff2labels <FEATURES> <PATTERN> <ATTRIBUTE> <COLOR> <GFF> ].

A useful script that allows you to filter a GFF file and create a “circos label file” with desired inputs. Eg. plot_circos --gff2labels CDS arcA ID red ecoli_k12.gff.

The example command will get each line where the feature (3rd column) is a CDS, that has the “acrA” (in the complete line) pattern to write the “circos labels file” using the ID attributes column as label (string as found in the gff), giving these features a “red” color option.

Tip

For <FEATURES> and <PATTERN> users can use “” to match anything, and “|” to match more than one string. E.g. plot_circos --gff2tiles "" "acrA|mdt" red ecoli_k12.gff.

For a better understanding see the Quickstart.

gff2tiles

Activated with --gff2tiles parameter.

Syntax: plot_circos [ --gff2tiles  <FEATURES> <PATTERN> <COLOR> <GFF> ].

A useful script that allows you to filter a GFF file and create a “circos tiles file” with desired inputs. Eg. plot_circos --gff2tiles CDS arcA red ecoli_k12.gff.

The example command will get each line where the feature (3rd column) is a CDS, that has the “acrA” (in the complete line) pattern to write the “circos tiles file” giving these features a “red” color option.

Tip

For <FEATURES> and <PATTERN> users can use “” to match anything, and “|” to match more than one string. E.g. plot_circos --gff2tiles "" "acrA|mdt" red ecoli_k12.gff.

For a better understanding see the Quickstart.