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The Ф24B genome was compared to other sequenced Stx phages and the archetypal lambdoid phage, lambda, using the Circos genome comparison tool and a PCR-based multi-loci comparison system.
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CNV calls were visually inspected by plotting the relative coverage of each genome using the Circos software [ 50].
MIRA-Seq data was also used to construct a heat map of the bovine fibroblast methylome using the Circos software package to illustrate the genome-wide nature of DNA methylation.> -wrap-foot> *Data obtained by MIRA-Seq and presented as fold difference in read count of methylated regions.
Circular representation of the genome was produced using the Circos software [27].
Using the Circos software [ 37], we represented the genome-wide distribution of putative chimeric mRNAs in Figure 1.
A graphical representation of the classical Bordetellae pan-genome was created using the Circos software [ 21].
Circular visualization of genome data was performed using the circos package (www.circos.ca, last accessed November 8, 2013) (Krzywinski et al. 2009) and graphically edited with the GIMP-package (www.gimp.org, last accessed November 8, 2013).
Circular maps for the two main replicons CHR1 and CHR2 (Figure 1) were drawn using the Circos software [214].
The graphical comparative maps were drawn using the Circos program.
Synteny was visualized using the Circos software [ 77].
Using the Circos program to display the number of reads per TA site [ 48], we visually confirmed randomly distributed insertions throughout the length of the genome.
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