Deep Assembly Variation Analysis


Assembly of gene amplicons and transcriptomes can produce coverage depths of many thousands of sequences.   NGen can accurately and rapidly assemble sequences to great depth of coverage so that variation analysis is possible. 


Strategy View (click to enlarge image)
Strategy View


The strategy view shows areas of very high coverage corresponding to highly expressed exons. Features from the reference sequence can be transferred over to the strategy view consensus so that coverage peaks can be correlated to specific feature annotations. If an expression value needs to be calculated, DNASTAR offers the QSeq application in the ArrayStar suite that complements the NGen package.


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SNP Statistics Report

 

The interactive SNP report is filterable to separate spurious background noise from SNP variations of interest. The SNP Percent Filter allows the researcher to eliminate putative SNPs by percent occurrence so that they do not appear in the SNP report. Quality thresholds can also be applied so that SNPs occurring at base calls of low quality do not appear in the SNP report. The SNP report also indicates if SNPs occur within a feature annotation and if in a coding region, the possible resulting codon change that incurs as a result of the variation

 


Sequence Assembly View

Sequence Assembly View

 

When a SNP is highlighted in the report, the SNP column is also highlighted in the sequence assembly view.



Additional information on Reference-Guided Genomic Assembly

Additional information on de novo Genomic Assembly

Additional information on RNA-Seq, SAGE and DGE Data Assembly