In this presentation an overview was provided of the NGS resequencing projects as ran in daily routine at KeyGene.
KeyGene uses Genalice Map in all high-volume re-sequencing projects as standard workflow for NGS secondary data analysis. To illustrate the power of the new Population Calling module, the analysis of 3,000 rice accessions was presented at the workshop. On a single node, the mapping and population calling was completed in just over 100 hours; mapping in 1:30 minute and population calling in 34 seconds per sample only.
Before the Population Calling module became available, KeyGene used a Genalice Map based stepwise approach to perform this type of multi-sample variant detection, which sped-up the workflow in comparison to BWA/GATK already ten-fold. Now with the new Population Calling module, the process became once again 30 times faster. Moreover, it was shown that the analysis time scales linearly with the number of samples.
Conclusion on NGS secondary data analysis, presentation KeyGeneThe approach is very flexible too, as incremental addition of samples to the total pool is possible. Extracting variants from low footprint and easy-to-query Genalice Variant Map (GVM) appeared very efficient and the VCF output conform standard.