DNASTAR’s Lasergene Genomics Suite offers the most accurate, fastest, and easiest-to-use pipeline for next-gen sequence alignment and variant calling. The DNASTAR validation control workflow used in conjunction with “gold standard” reference materials enables you to evaluate the sensitivity, specificity, and balanced accuracy of your project.
The results? Our results demonstrate that SeqMan NGen has fewer false negatives and better sensitivity compared to each of the other four workflows tested. SeqMan NGen also aligns exome data and performs variant calling an average of 3.5 times faster than the alternative pipelines: BWA+GATK, CLC Bio's Genomics Workbench, and Geneious.
SeqMan NGen vs. GATK: This evaluation compared Illumina whole exome alignment results from SeqMan NGen 12.2 to two industry-leading pipelines: the BWA read-mapper in combination with the Broad Institute’s Genome Analysis Toolkit (GATK) Unified Genotyper variant caller, and the BWA read-mapper in combination with the GATK Haplotype Base Caller.
Results demonstrate that SeqMan NGen achieves higher sensitivity for each data set tested, compared to the BWA+GATK pipelines. In addition, SeqMan NGen analyzes variants in whole exome data an average of 5 times faster than the BWA+GATK workflows. The results from this comparison show that SeqMan NGen is a fast, high accuracy read-mapper/variant caller for Illumina sequencing data.
SeqMan NGen vs. CLC Bio Genomics Workbench: This evaluation compared Illumina and Ion Torrent whole exome alignment results from two aligners: DNASTAR’s SeqMan NGen 12.2 and CLC Bio’s Genomics Workbench 8.0.
Results demonstrate that SeqMan NGen has higher sensitivity, finds fewer false positives, fewer false negatives, and has a lower false discovery rate compared to CLC Bio’s Genomics Workbench 8.0. For Ion Torrent exome data, SeqMan NGen has better specificity, reports fewer false positives, and has a lower false discovery rate. For both types of data, SeqMan NGen performs variant analyses from 1.5- 4.0 times faster than Genomics Workbench.
SeqMan NGen vs. Geneious: This evaluation compared Illumina and Ion Torrent whole exome alignment results from two commercial aligners with variant detection workflows: DNASTAR’s SeqMan NGen 12.2 and Geneious 8.1.
Results demonstrate that SeqMan NGen has fewer false positives, fewer false negatives, a lower false discovery rate, and higher sensitivity and specificity compared to Geneious 8.1. SeqMan NGen is also an average of nearly 4 times faster than Geneious at performing variant analysis.