Services:

-          Genome Alignment (cellular and viral)

-          De novo assembly

-          Differential gene and/or isoform expression analysis (statistics using edgeR)

-          Fusion gene discovery

-          Nucleotide sequence variation identification

-          Microbiome analysis

-          microRNA seed identification (find all microRNA seeds within any genome and provides output for visualization on genome browser and data on seed localization on all gene features)

-         Circular RNA identification

-         Data transfer (uploading data to sequence databases/archives)

 

Methods:

-          Aligners

o   Novoalign

o   Tophat/Bowtie

-          De novo assemblers

o   Abyss

o   Velvet

o   SOAP (pending)

-          Fusion gene identification

o   FusionSEQ

o   TopHat-Fusion

-          Read visualization

o   Integrated Genome Viewer

-          Blast (Local, batch)

o   Non-restricted nucleotide database

-          Gene and isoform level RPKM analysis

o   SAMMate

o   Cufflinks

o   CummeRbund

-          Clinical sequence handling

o   DCBI decrypt (for decrypting patient sequence data from NCBI)

o   Fastq dump (for converting NCBI "sra" formatted sequencing data into "fastq" format for sequence analysis)

o   Aspera - for available bandwidth conscious ultra fast transfer of large volumes of data over the internet.

o   Local Galaxy (PSU) server for secure file processing.