Data Analysis

As a Vironomics Core, we not only perform the assay services that generate data, but we also offer analysis services to assist transforming the raw data into ready-to-use data.

qPCR

Analysis of the raw qPCR is not included in the assay cost; however, we do offer a data analysis/consultation service that can assist you with analysis or creating ready-to-publish figures. Please contact Dr. Dirk Dittmer and/or the Vironomics Core Manger for this service and estimated turn-around time.

454 GS Junior next-generation sequencing

For the Roche 454 GS Junior next generation sequencing data, we use both commercial software and open source software for data analyzation. Below is the summary of the frequently used software:

CLC genomic workbench is a commercial software for analyzing and visualizing next generation sequencing data; it includes a number of features within the fields of genomics, transcriptomics and epigenomics. The CLC supports all major next generation sequencing platforms and read mapping as well as de novo assembly of hybrid data.

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole genome shotgun sequencing. Celera Assembler has enabled many advances in genomics, including the first whole genome shotgun sequence of a multi-cellular organism (Myers 2000) and the first diploid sequence of an individual human (Levy 2007). Celera Assembler was developed at Celera Genomics starting in 1999. It was released to SourceForge in 2004 as the wgs-assembler under the GNU General Public License. The pipeline revised for 454 data was named CABOG (Miller 2008)

Newbler is the assembly/mapping program developed by 454 Life Sciences for of 454 data, it is in fact the core of both the gsAssembler/GS De Novo Assembler (GUI based), gsMapper/GS Reference Mapper Software /GUIbased), runAssembly (command-line based) and gsMapper (command-line based). It uses k-mer based hashing and the 'overlap-layout-consensus' approach. Takes both shotgun and paired end reads.