Metagenomics

GenomeQuest’s Metagenomics application allows you to compare millions of sequences against all of the world’s reference data to determine the composition of the DNA in the sample. It has been used in infectious disease applications, diagnostics, air quality, soil change over time, defense applications, and indeed, to rescue the California Syrah grape from decline symptoms due to a previously unknown virus.

It features:

  1. Support for all sequence types. It works regardless of whether you have 454 reads, Pacbio reads, Illumina, or SOLiD reads (although you get better specificity with longer reads).
  2. Characterization of sample by species, taxonomy, and database. GenomeQuest allows you to see in clear pictures which species are found inside of your sample, and allows to extract the reads that hit to those species for further analysis.
  3. Novel DNA. Reads that hit to no reference sequence are collected and available for further analysis.
  4. Assembly. Extraction of reads that hit to any species, or those that hit to nothing, can be pushed right into the Newbler or Velvet assembly programs, also hosted right on the GenomeQuest service.
  5. Continually updated reference data. All reference data to which you compare your sample has the benefit of GenomeQuest’s constant scouring of public data sources, and is updated on a nightly basis.
  6. Your own reference data. If you have proprietary reference data that you want to compare your metagenomics sample to, simply upload it and it is immediately available in the Metagenomics application – but only for you.

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).