March 3, 2017

Pistoia Alliance Sequence Squeeze Competition Announces Final Judge and First Competition Entry

The Pistoia Alliance, a precompetitive alliance of life science companies, technology vendors, publishers, and academic groups, announced that it has selected the final judge for its Sequence Squeeze Competition.

The competition, which was launched in October, offers bioinformaticians, mathematicians, physicists, and computer scientists the chance to win US$15,000 for developing the best new algorithm for compressing next-generation sequencing (NGS) data.

 Tim Fennell, assistant director for sequencing pipeline informatics at the Broad Institute, will serve as the fourth judge for the competition. Fennell and his team develop and maintain the Java language bindings for the popular SAM and BAM file formats as well as the Picard suite of tools for working with NGS data. Fennel joins three previously announced panelists: Guy Coates, information systems lead at the Wellcome Trust Sanger Institute; Yingrui Li, duty operation officer of the BGI; and Nick Lynch, external liaison and past president of the Pistoia Alliance.

 The competition received its first entry in October from the Wellcome Trust Sanger Institute. Full details on the performance of all competition entries are being tracked on the competition leaderboard at the competition website at

"Compression is a major problem in the management of NGS data, and our judging panel now comprises experts from the three most respected global institutes in gene sequencing---- there's no one better qualified to evaluate the entries in this competition," said Michael Braxenthaler, president of the Pistoia Alliance. "Now it's a question of spreading the word about the competition. We need a diversity of thinking if we're going to develop truly novel methods for compressing NGS data."

The competition requires entrants to devise and implement a computer algorithm for compressing and then decompressing sequencing data stored in the commonly used FASTQ format. Entries must be fully open source so that the entire scientific community can benefit from the winning algorithm. The competition closes on 15 March 2012 and is administered on the Pistoia Alliance's behalf by Eagle Genomics Ltd., an outsourced bioinformatics services and software company. For full details on how to enter, and to submit an entry, please visit

Topics: Announcements, Bioinformatics