NextGENe® software has been developed specifically for use by biologists performing whole genome or targeted resequencing projects containing single nucleotide polymorphism (SNPs) insertions/ deletions (INDELs) and large structural DNA rearrangements in sequencing data from Ion Torrent PGM & Proton™, Roche Genome Sequencer FLX/Junior, Illumina platforms; Life Technologies Applied BioSystems' SOLiD™ System and PacBio platforms. NextGENe's Windows® based operation removes the complexity found with programs such as CLC bio, Lasergene's SeqMan & NGEN, MAQ & SOAP, Top Hat, BWA & Bowtie. Biologists simply input the systems raw reads or BAM files, select the application and click go to begin analysis. Pooled or barcoded samples are quickly de-multiplexed by utilizing the included Barcode Sorting tool, which will separate out each pooled sample for subsequent analysis. NextGENe's Pipeline Tool, AutoRun can be used to set up an unlimited number of consecutive analyses on an unattended basis. Upon completion results are presented in NextGENe's annotated whole genome browser/viewer for review/editing/commenting.
NextGENe features up to 99% accuracy, INDEL detection up to 33% of read length, rapid review of DNA variants, nucleotides, and Amino Acids. The software also includes a host of filtering options, variant confidence scoring, multiple analysis comparison capabilities, hyper links to dbSNP / GenBank and possible causative prediction.
Structural Variants (SVs) include insertions, deletions, inversions, gene fusions, and copy number variants that frequently occur across the human genome with over 1000 segmental deletions and over 200 copy number polymorphisms having been reported. These genomic structures have been shown to be important in a number of diseases, usually referred to as genomic disorders.
NextGENe allows large mismatches when aligning to the genome in order to find SVs and display information about those regions in a structural variation report. The structural variation report uses a specialized algorithm to list regions with high variant frequency. Interference from false positives caused by sequencing errors is rarely detected in this report since multiple errors are unlikely to occur in a local region.
NextGENe then generates pseudo-paired reads for the sequences aligned to these regions by breaking the original reads into pairs. These can be aligned to the reference genome in order to map the SVs.
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