What is SeqAlto?

SeqAlto is an aligner specifically designed for Illumina reads of length greater or equal to about 100-bp. It takes advantage of this longer read length to provide fast alignment rates and accurate placement of polymorphic reads. Paired-end reads are recommended for even greater accuracy. When aligning 100-bp paired-end reads SeqAlto is on average about 2-4x faster than BWA while being more sensitive and much faster for longer reads. Alignment of Ion Torrent/454 reads is in development.

A commercially-available and fully-supported version of SeqAlto called "Bina Aligner" is available from Bina Technologies and includes additional performance enhancements added by the team at Bina. Please contact Bina Technologies at info@binatechnologies.com for more information on the Bina Aligner. In addition, the Bina team welcomes inquiries for academic collaborations and scientific co-development.

The following is a comparison of the performance when aligning 85 Million 101-bp paired-reads. The benchmark was run with 8 threads on AWS.


John C. Mu, Hui Jiang, Amirhossein Kiani, Marghoob Mohiyuddin, Narges Bani Asadi and Wing H. Wong, Fast and Accurate Read Alignment for Resequencing, Bioinformatics, 2012 [online]

7/1/2012 - Beta release

Fixes some bugs from the initial release mainly pairing read across chromosome boundaries and alignment of indels.


5/15/2012 - Initial release (0.5-r117)

This is the version reviewed with the paper. There are some known issues.