FANSe3 is the third generation of FANSe series mapping algorithm, which maps millions and billions of sequencing reads to reference sequences. Unlike the other NGS mapping algorithms, which prioritize the speed and then try to compensate the accuracy, the FANSe series algorithm is prioritized to guarantee the accuracy and robustness, and using computational optimization to speed up. Click here to watch the TED talk by the inventor of FANSe, Dr. Gong Zhang, to recognize how the accurate FANSe outperformed the other algorithms and really saves lives. It also played an important role in the Human Proteome Project to analyze all the translatome sequencing data, which is one of the key resource pillar of HPP.

Inherited the extremely high accuracy and robustness from FANSe2, FANSe3 is 30-200x faster than FANSe2 in most cases. With the up-to-date server nodes, FANSe3 can map 30x human genome sequencing data to human hg19/GRCh37 reference genome within half an hour, in a single desktop computer. This speed means that the bottleneck is often the disk I/O, not the CPU any more, especially in the transcriptome and exome sequencing applications. A lot of other features are also included in the FANSe3, e.g. efficient indel support, unique mapping, efficient unmasked reference genome support, direct read trimming.

FANSe3 is programmed using Visual BASIC.NET and designed exclusively for specialized supercomputing infrustructure. Optimized thoroughly for many-core system, it requires enourmous amount of memory (128GB or more) to be that efficient. The Next-generation Sequencing Analysis Cloud System "Chi-Cloud", established and operated by the Chi-Biotech Co. Ltd., has been implemented the FANSe3 algorithm in the commercialized to process thousands of NGS datasets per week since late 2016. For your convenience, you can directly use the Chi-Cloud to analyze your NGS data with just a few mouse clicks and do not need your local computational power.

FANSe3 is an industrial development project of Chi-Biotech Co. Ltd. For commercial usage, please contact Chi-Biotech to obtain a licence.



  • TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data. Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D206–D212
  • Another FANSe3 article in submission