Faster Alignment of Longer indels

A substantial and important part of genetic variation amongst individuals and in diseases such as cancer is caused by insertions and deletions (INDELs). Alignment and detection of INDELs in short read NGS data analysis is very complex, as it requires mapping software to identify gaps in the alignment solution.

GENALICE MAP can align reads with “infinite” gap sizes at high speed due to its architecture, algorithms and comprehensive reference index. This enables it to detect much longer INDELs (>10 bases) than BWA-MEM/GATK, a widely used alignment method.

In addition, the long INDELs detected by GENALICE MAP better reflects sequence variation in the cancer genomes under study and reveal potential disruptive genetic alterations.

In this white paper you will learn:

  • What makes INDEL discovery challenging?
  • How GENALICE MAP aligns and detects longer INDELs?
  • Quality vs. processing speed

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