Services
Complete Genomics provides whole human genome sequencing and analysis as a service to academic and biopharmaceutical researchers at an unprecedented quality, cost, and scale without requiring investment in in-house sequencing instruments, high-performance computing resources, or specialized personnel.
Complete Genomics offers two primary services: the Standard Sequencing Service and the Cancer Sequencing Service, as described below. Additionally, Complete Genomics offers open source tools, Complete Genomics Analysis Tools (CGATM Tools), for optimized downstream analysis of complete data sets. See CGA Tools for more information.
The Complete Genomics Standard Sequencing Service provides whole human genome sequencing, with sophisticated assembly, variant detection, and annotation across all variation types including SNPs, indels, copy number variations (CNVs), structural variations (SVs), and mobile element insertions (MEIs). Customers send a plate of DNA samples and in return receive a data package of fully mapped reads, summary files of all variations found, and evidence files that support the variations.
Standard Sequencing Service Specifications:
- Minimum average coverage of either > 40x or >80x reads sequenced across the reference genome, depending on coverage level selected
- Complete diploid call in > 90% of unique loci of the reference genome
- Deliverables include sequence variants, functional annotations and data summary reports as well as the full set of supporting data for these results (reads, scores and mappings)
Because we have optimized our technology platform and our operations for the unique requirements of high-throughput whole human genome sequencing, we are able to achieve accuracy levels of 99.999% (Drmanac, Science 2010).
Assembly Pipeline Versions
| Assembly Pipeline Version | Key New Features * | Release Date | Status |
| 2.0 |
Improved sensitivity and specificity in small variants detection Updated small variant scoring approach Updated CNV and SV baseline genome sets Added event annotation for structural variations |
September 2011 | Available |
| 1.12 |
Added master variation file that aggregates variation calls and annotation information from various Complete Genomics export files Added mobile element insertion results |
May 2011 | Available |
| 1.11 |
Added coverage distribution and coverage by GC content for coding region of the genome Expanded reported summary statistics and metrics |
March 2011 | Unavailable |
| 1.10 |
Added genomic copy number results Added structural variation results |
November 2010 | Unavailable |
| 1.9 |
Added a wide range additional report files Expanded annotations to include ncRNAs and others |
September 2010 | Unavailable |
| 1.8 |
Added ability to choose NCBI build 36 or 37 as the reference genome Expanded annotations |
June 2010 | Unavailable |
| 1.7 |
Added a gene variation summary report Performed several file format improvements Improved base calling algorithm for more high quality calls |
January to May 2010 | Unavailable |
* Refer to the Release Notes for a complete list of new features.
Our Cancer Sequencing Service provides researchers with a valuable tool to further their understanding of cancer genomics. Samples are accepted as tumor-normal pairs or trios, reflecting how common cancer studies are designed. Algorithms in our Analysis Pipeline are tailored to handle the complexities of cancer samples, which are typically heterogeneous, non-diploid and include possible stromal contamination.
Each genome is compared to a reference genome and each tumor genome is compared to its matched normal sample. All germline and somatic variants are called, facilitating a much greater understanding of the genetic basis of cancer
The Cancer Sequencing Service provides:
- A choice of either > 40x or >80x reads sequenced across the reference genome
- Complete diploid calls in > 90% of the reference genome
- SNPs, CNVs, indels, SVs and mobile element insertions are called and full supporting reads, scores and mapping is provided.
Our Analysis Pipeline has been updated to reflect improved sensitivity and detection of small variants, including gene fusions and updated CNV and SV baseline germline sets. Somatic events for tumors ( small variants, CNVs and SVs) are available in Complete Genomics native file format and standard VCF*.
| Analysis Pipeline Version | New Key Features * | Release Date |
| 2.0 |
Somatic events for tumors (small variants, CNVs, and SVs), in both Complete Genomics native file format and standard VCF format Improved sensitivity and specificity in small variant detection, including non-diploid variants, such as those in the presence of tumor heterogeneity or aneuploidy Updated small variant scoring approach Updated CNV and SV baseline genome sets Added event annotation for structural variations, including gene fusions |
September 2011 |
* Refer to Release Notes for a complete list of new features.
Gain access to advances in sequencing without actually sequencing! Enhance your study by leveraging ongoing improvements in Complete Genomics' assembly pipeline. Alternately, make it easier to compare results across projects or samples by processing them through the same pipeline version.
Reanalysis Service:
- Reanalysis is available for genomes that were originally sequenced using Complete Genomics Assembly Pipeline version 1.5.0 or later
- Samples may be reanalyzed using the Standard Sequencing Service or the Cancer Sequencing Service, regardless of how they were originally submitted