Fig. 1

Overview of MoMI-G. A user typically selects one of the preset combinations of view modules. The user can customize the window by adding or removing view modules, if necessary. Three examples showing views of different scales are shown. Comprehensive descriptions for all modules are shown in Additional file 1: Figure S1. a Chromosome-scale view: Circos Plot (left) shows the distribution of SVs over all chromosomes. Arcs are chromosomes. Curves represent SVs. Feature Table (right) shows a filtered/sorted list of the SVs in an input VCF file. b Gene-scale view: SequenceTubeMap (top) shows the graphical view of the genomic region selected in Circos Plot, Feature Table, or Interval Card Deck. A rounded rectangle is a node that represents a piece of a genomic sequence. The thick lines spanning over nodes are paths; the horizontal thick black line with light/dark shades is a chromosome of the reference genome (a reference path); the blue line indicates an SV path that corresponds to a VCF record that represents one end of an inversion. The color of lines indicating SVs is assigned arbitrarily. Read alignment paths can be shown as gray thin lines when the read alignment information (BAM or GAM file) is provided. The inversion here is likely heterozygous. Read alignment paths are not shown in most examples shown in this paper for simplicity. Nucleotide-level alignments can be also shown on the read alignment paths if the input data contains the base-to-base alignment information (Additional file 2: Figure S2). Interval Card Deck (bottom) queues a list of genomic intervals for candidate SVs selected by using Circos Plot or Feature Table for rapidly screening hundreds of candidate intervals. c Nucleotide-scale view: SequenceTubeMap can show nucleotides