GENALICE MAP Processes Entire Genome in 30 mins

GENALICE announced an upgrade to its Next-Generation Sequencing software the GENALICE MAP, capable of processing the entire human genome in 30 mins.

The GENALICE MAP DNA data processing software along with short read alignment also features 5-min Variant Calling. MAP comes installed in the company’s GENALICE VAULT, a hardware-software tool which uses a dual Intel Xeon E5 server for processing.

MAP combines short read alignment with variant calling, mastering both steps in less than 30 mins on human genome with a 40x depth. It also allows real time access of exome data or panels. Other software running on the same hardware usually take around 24 to 48 hour using Burrows- Wheeler Aligner (BWA) and the Broad Institute’s GATK variant calling software.

Ultra-fast & Accurate

MAP in comparison to BWA-MEM/GATK was shown to be 100 times faster for human genomes and 57 times faster for cultivated Tomato genome. The algorithms are especially designed to run on new hardware. Accuracy comes from the recently added variant caller in MAP, which in tests was able to identify 98% of SNPs, whereas BWA-MEM/GATK identifies around 95%.

Easier to Use & Cheaper

The MAP workflow is short and simple to follow, with two major steps: alignment and variant calling. While alignment handles sorting, aligning and writing to disk; variant calling handles marking duplicates, INDEL realignment, genotyping and filtering in one step. Results can be produced in more efficient GAR or GENALICE Aligned Reads format, replacing the bigger and older BAM and FASTQ files. The result is a 100-fold reduction in storage space. While a FASTQ format file for cultivated tomato is around 88GB, the same in GAR is 1.6GB.

MAP will help researchers save a lot of time and energy on processing and also in saving and transferring the processed genomes. According to GENALICE CEO Hans Katen, “Combining our speed and footprint reduction we are able to drive down the cost of processing and storing a full genome to less than $100 per year, while further improving the quality”. GENALICE has already signed a contract with NIHR Oxford Biomedical Research Center for supplying them with GENALICE VAULT appliance, which comes with MAP installed.