Abstract:
In many applications of NGS, sequenced samples contain multiple distinct but sometimes very similar sequences. This talk addresses two such applications: reconstructing viral quasispecies from shotgun and amplicon reads and transcriptome reconstruction from RNA-Seq single and paired reads.

Error-prone replication of RNA viruses with high mutation rate creates a diverse population of closely related variants known as quasispecies.  By understanding the quasispecies, more effective drugs and vaccines can be manufactured as well as cost-saving metrics for infected patients implemented.  Reconstructing the quasispecies spectrum is difficult since conserved regions in the genome can extend beyond the read length. We will compare recent approaches of quasispecies reconstruction from shotgun and predefined amplicon reads. 

We will next address computational issues in gene differential expression and isoform quantification from RNA-Seq reads. A novel bootstrap-based method for gene differential expression is compared with other existing statistical approaches. Finally, a simulation regression.method for transcriptome quantification is described..
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