Whole Genome Analysis

The GenomeQuest Whole Genome Analysis suite finds and annotates genomic variation. Features include:

WGA

Whole Genome Analysis

  1. Arbitrary scale. Works for whole genomes, exome capture and targeted resequencing data
  2. Support for mismatches and indels. Generalized gapped alignments allow for identification of mismatches and indels.
  3. Exposed Parameters. Variant calling is performed using easy-to-understand, easy-to-adjust heuristic parameters
  4. Total vendor support. All popular sequencing vendors supported, including native alignments in SOLiD colorspace, support for Pacific Bio reads, and all of the others.
  5. Import external variants. GenomeQuest supports many external variant calling formats, including BGI’s variant calls, VCF, Complete Genomics, and SVA.
  6. Arbitrary reference genome. Upload and use your own reference genome if it’s not among the large number of references already available in GenomeQuest.
  7. Powerful included annotation. Annotate all variants using a large collection of always up-to-date reference databases, from dbSNP to pharmGKB, to cosmic somatic mutations, to gene models, and beyond.
  8. Your own annotation. Annotate genome-wide variants with your own proprietary locus-specific content.
  9. Predict impact of variation. Find protein impact like synonymous and non-synonymous amino acid changes, frame shifts, pre-mature stops and amino acid indels.
  10. Interact. Find the 30 variants that impact proteins associated with your science that no one has ever discovered before, literally in one-click in web site.

GenomeQuest Applications

All GenomeQuest science applications are delivered in an easy-to-use, integrated environment. They package all bioinformatics details – including read and reference data, scientific algorithms, all third party integration, all parameters, and the compute environment – into a simple form-based interface. Users query results using an interactive sequence browser. All data, parameters, and results can be shared with colleagues and teams using the GenomeQuest collaborative environment.

GenomeQuest applications are built to scale to thousands of samples, each with billions of reads. They support all popular sequencing machines (including Illumina, SOLiD, 454, and PacBio) and all common formats (including FASTQ, FASTA, SAM/BAM, VCF, SVA, and others).

Details on the Wiki