Graphical genome maps are widely used to assess genome features and sequence characteristics. The CGView (Circular Genome Viewer) software family is a popular collection of tools for generating genome maps for bacteria, organelles and viruses. In this review, we describe the capabilities of the original CGView program along with those of subsequent companion applications, including the CGView Server and the CGView Comparison Tool. We also discuss GView, a graphical user interface-enabled rewrite of CGView, and the GView Server, which offers several integrated analyses for identifying shared or unique genome regions relative to a collection of comparison genomes. We conclude with some remarks about our current development efforts related to CGView aimed at adding new functionality while increasing ease of use.

SUMMARY: NGS-SNP is a collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of whole genomes from any organism with reference sequences in Ensembl. Included among the annotations, several of which are not available from any existing SNP annotation tools, are the results of detailed comparisons with orthologous sequences. These comparisons can, for example, identify SNPs that affect conserved residues, or alter residues or genes linked to phenotypes in another species. AVAILABILITY: NGS-SNP is available both as a set of scripts and as a virtual machine. The virtual machine consists of a Linux operating system with all the NGS-SNP dependencies pre-installed. The source code and virtual machine are freely available for download at http://stothard.afns.ualberta.ca/downloads/NGS-SNP/. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.