There are many commercial and open source software packages that complement Complete Genomics sequencing services to allow you to further explore and visualize your data. The table below lists third-party software providers and the tools they have developed to support Complete Genomics data.*
| Tool | Organization(s) | Category | License | Details |
| Annovar | U. Penn/UCSD | Annotation | Free (open source) for nonprofit use | A software tool that functionally annotates genetic variants with gene, region, and filter-based annotations. |
| Circos | Martin Krzywinski (Michael Smith Genome Sciences Centre) | Visualization | Free (licensed under GPL) | A tool for visualizing genomic data (including alignments, copy number, and structural variation) in a circular ideogram format. |
| DNAnexus | DNAnexus, Inc. | Analysis, Filtering, Storage, Visualization | Commercial | Cloud-based suite of NGS analysis and visualization tools. The Complete Genomics 69 public genomes are pre-loaded for browsing. |
| Galaxy | Penn State, Emory University | Analysis | Academic (free) | A web-based NGS analysis suite. For a tutorial on using Galaxy with Complete Genomics data, visit this link. |
| Genome Trax | BIOBASE | Annotation, Filtering | Commercial | Web-based annotation service, containing comprehensive rare disease variants from HGMD professional, regulatory sites from TRANSFAC professional, disease genes from PROTEOME. |
| GenomeQuest | GenomeQuest, Inc. | Analysis, Annotation, Filtering, Storage | Commercial | Cloud-based research platform for genomic-scale data analysis. |
| IGV – Integrative Genomics Viewer | Broad Institute | Visualization | Academic (free) | Visualization of genomic data. Complete Genomics reads and mappings from the MAP and EVIDENCE folders must be converted to BAM using CGA Tools map2sam or evidence2sam, and SAMtools. IGV can also import BED tracks and wiggle plots made from CNV data using a perl script from the Complete Genomics Tool Repository (v1.12 only). |
| Ingenuity Variant Analysis | Ingenuity Systems, Inc. | Analysis | Commercial | Variant filtering and genome comparison software. |
| Kaviar | Institute for Systems Biology | Annotation | Academic (free) | Compiles SNVs observed in humans. A web interface is available, but for annotation of large lists of variants, download the database and tools to run locally. It requires as input a list of chromosomes and coordinates, and returns the count for different alleles among the genomes it references. |
| PLINK | Center for Human Genetic Research, Massachusetts General Hospital, the Broad Institute | Analysis | Academic (free) | Good for cryptic relatedness, ethnicity calculations, or stats in PLINK. |
| PLINK/Seq | Analytic and Translational Genetics Unit at Massachusetts General Hospital | Analysis, Annotation, Filtering | Academic (free) | An open-source C/C++ library of analytical tools for human genetic variation data from whole-exome and whole-genome studies. |
| SAM Tools | Wellcome Trust Sanger Institute, Broad Institute, Beijing Institute of Genomics, UCLA, Boston College, University of Michigan, 1000 Genome Project Data Processing Subgroup | Format conversion | Free (open source) | Accepts SAM files as input for conversion to BAM and also sorts and indexes BAMs for viewing in IGV. The CGA Tools evidence2sam and map2sam provide conversion from various Complete Genomics data formats to the SAM format. |
| SVS 7.5 – SNP & Variation Suite | Golden Helix, Inc. | Analysis, Filtering, Visualization | Commercial | A collection of rare variant analysis tools for whole genome sequencing data. For a video tutorial on variant classification and visualization featuring Complete Genomics data, visit this link. |
| UCSC Genome Browser | UC Santa Cruz | Visualization | Academic (free) | Visualization of genomic data. Upload data to Genome Graphs, in a one line per marker format (i.e. chromosome, position, value). For details on importing data to Genome Graphs, visit this link. |
| VAAST | University of Utah | Analysis, Annotation, Filtering | Free license for academic use | Computational tool for identifying disease-causing mutations by individual genome sequencing. The tool allows for the prioritization of single nucleotide variants to identify those that are likely to be involved in disease. |
*Please note that unlike CGA™ Tools, these open-source platforms, scripts or executables listed are not formal product offerings from Complete Genomics, and as such are not fully supported by our company. Any usage of these items should be kept in mind.