Commercial-scale Genome Center

Complete Genomics’ innovative sequencing technology will be uniquely offered as a service through its own commercial-scale genome center. Customers will have access to large-scale, complete human genomic data analysis without making a major in-house investment in instruments or high-performance computing resources.

This page contains information for developers.

Bug reports, source contributions or modifications, questions, or other correspondence should be sent to dev-support@completegenomics.com. Complete human genome sequences are provided to our customers in a variety of formats. The Application Programming Interface (API) is intended to simplify access to genomic sequence data stored in the Complete Genomics file formats. This API supports access to several types of data, including:

• Reads - called bases and quality scores
• Empirical estimates - gap distribution and score-to-accuracy
• Alignment - mapping to a reference sequence
• Variations - called consensus variations

This API is delivered as a set of C++ source code files that can be compiled to produce a statically linkable library for accessing and using data delivered by Complete Genomics to its customers. The API contains full source level documentation as well as a description of the file formats. The API contains a set of demo data that can be used for development and testing purposes. This version of the API contains some changes to the documentation and provides a new example program. The docs now include a tutorial on the APIU and the new example program will convert the reads and scores to a fastQ formatted file, that converts the scores to PHRED-LIKE scores. See the file Version Notes for a list of changes to the API.
NOTE: This version of the API is NOT compatible with the reference genome data as supplied on the disk drives released prior to Jul 15th. Continue to use the version of the API that is provided with the data on the disk drives.

Download the API (50 MB)

Read the version notes

File Format documentation (PDF) The API is licensed in source form under the terms of the Apache Version 2.0. To review the full terms of this license please read the contents of the LICENSE.txt file found within the software distribution which contains this file or read the license of the website from apache.org.