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Compatible Third-Party Tools
Compatible Third-Party Tools
Compatible third-party software tools that 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. Input a list of variants containing chromosome, start position, end position, reference nucleotides and observed nucleotides. In return, the tool provides gene-based annotations, region-based annotations 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 and structural variation, using a circular ideogram format. The format of the input file can be as simple as: chr, start, end, value. |
| Complete Genomics Scripts | Complete Genomics | Format Conversion, Visualization | Free | A series of scripts designed to manipulate and output data useful for further analysis or for use in other software packages. |
| DNAnexus | DNAnexus, Inc. | Analysis, Filtering, Storage, Visualization | Commercial | Cloud-based NGS analysis and visualization tools. Upload ASM folder and work with variant results, CNV results and SV results on separate tracks. 69 additional Complete-sequenced public genomes also viewable. |
| Galaxy | Penn State, Emory University | Analysis | Academic (free) | A web-based NGS analysis suite. Import the mastervar file. 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. Imports Complete Genomics Variations files (or a filtered subset) for analysis. |
| GenomeQuest | GenomeQuest, Inc. | Analysis, Annotation, Filtering, Storage | Commercial | Cloud-based research platform for genomic-scale data analysis. Import variation results for analysis. |
| IGV - Integrative Genomics Viewer |
Broad Institute |
Visualization | Academic (free) |
Imports .BAM files created in SAMTools from CGATools outputs of evidence2sam or map2sam. Also, it can import a .BED track and wiggle plot made from CNV data using a perl script from the Complete Genomics User Community, which you can download here. |
| JMP Genomics | SAS | Analysis, Visualization | Commercial | The JMP Complete Genomics Input Engine imports variant, dbSNP, and gene variant summary files from ASM directories and combines similar files from different samples into a single tall SAS data set per chromosome. .bz2 files must be uncompressed before running the input engine. |
| Kaviar | Institute for Systems Biology | Annotation | Academic (free) | Compiles SNVs observed in humans. It requires as input a list of chromosomes and coordinates, and returns the count for different alleles among the genomes it references. A web interface is available, but for annotation of large lists of variants, download the database and tools to run locally. |
| PLINK | Center for Human Genetic Research, Massachusetts General Hospital & the Broad Institute | Analysis | Academic (free) | Good for cryptic relatedness or ethnicity calculations or stats in PLINK. You can find a perl script for creating a set of PLINK files from CGA Tools testvariants output on the Complete Genomics User Community here. |
| PLINK/Seq | Analytic and Translational Genetics Unit at Massachusetts General Hospital | Analysis, Annotation, Filtering | Academic (free) | Import .VCF files which can be created using scripts from the Complete Genomics User Community. |
| The R Project | Worldwide contributors | Analysis, Visualization | Free (open source) | A language and environment for statistical computing and graphics. Bioconductor is an R subproject focused on analysis of high-throughput genomics data. Visit this link for details on using Bioconductor with sequence data. Also, the Complete Genomics User Community contains several R-based scripts. |
| 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. Also sorts and indexes BAMs for viewing in IGV. The CGA Tools modules 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. Import Complete Genomics var-[ASM-ID].tsv files. Can import one or multiple at a time. 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) | 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. VCF files generated using scripts from the Complete Genomics User Community can be converted to the required input format (GVT) by the vaast_converter tool. |