Displaying reference mappings

Figure 2.32: The reference mapping component showing alignment results for a metatranscriptome dataset mapped to the reference genome of one of the dominant organisms. From top to bottom, the component displays a) navigation and coverage histogram, b) currently selected interval and c) aligned DNA sequences for the interval. Color coding refers to relative sequence identity.

Figure 2.33: An alternate visualization mode is the generation of fragment recruitment plots, here showing the same data as described previously (2.32). The view mode features the fragment recruitment plot itself and additionally provides stacked bars summarizing mapping identity within reference intervals, grouped into low (red), medium (yellow, $\ge$ 75%) and high (green, $\ge$ 97%) quality mappings.

Alignment of metagenome or metatranscriptome data to reference sequences of known origin allows researchers to evaluate relative identity between metagenome sequences and the actual strain or to obtain an overview of gene expression within a meta-transcriptome. MGX currently provides predefined pipelines employing BLAST [Altschul et al., 1990], FR-HIT [Niu et al., 2011] and Bowtie 2 [Langmead and Salzberg, 2012]. The reference mapping component is provided to inspect and browse alignment results, offering both a generic alignment view where each mapped sequence is colored according to mapping identity, as well as a fragment recruitment view. Switching between view modes is possible from the context menu of the mapping component.