DNA-Seq – Finding genomic variants and understanding their downstream effects
The detection of SNPs and structural variants depends on good read quality and a reliable mapping approach. The Genomatix mapper aligns reads with a multi-seeding approach, leading to high sensitivity and specificity. For each mapping we report reads that map uniquely to the genome but also reads that map multiple times or even ambiguous. To support the detection of structural variants, spliced-alignments are used allowing to map individual reads to different chromosomes.
After the mapping different genomic variants are detected, these are: homozygous and heterozygous SNPs and InDels, structural variants and copy number variations (CNVs). SNPs are categorized into: initiating, missense, nonsense, read-through, (non)-synonymous or changes in TF binding sites. CNV regions can be detected in our copy variant visualizer, where multiple conditions can be compared. The structural variant detection is based on paired-end sequencing.
SNPs, InDels, CNVs and structural variants can all affect gene regulatory pathways and signaling networks. Thus, to understand the biological implications we offer a whole suite of downstream analysis tools for gene regulatory networks, gene enrichments, pathways and networks.