Software developed by Boston College lab delivers speed and accuracy to genome research

A second Nature Methods article, written in collaboration with colleagues from the Washington University School of Medicine, reported that three other computer programs developed by the Marth lab made it possible to quickly and accurately examine the whole genome of a laboratory worm and identify key differences between the sample strain and an earlier strain – a comparative process known as re-sequencing, now being applied to the genomes of humans and other organisms. This second study used another next-generation DNA sequencing platform, the Illumina/Solexa machine.

Advances are driving re-sequencing costs down, but researchers must still prove the effectiveness of the new technology by working with smaller organisms, which made the worm study critical, Marth said. “This brings us closer to a major milestone in human individual re-sequencing – the decoding of the genome of human beings in routine fashion,” said Marth.

Of the few computer programs available for the new sequencing machines, the software package developed by the Marth lab is the only one capable of working with a variety of decoding machines and offers greater accuracy, allowing researchers to separate true genetic variations from data errors, said Marth. PyroBayes, a Linux-based package, is made available to fellow academic researchers at no cost.

As a member of its analysis group, the Marth lab participates in the data analysis of the 1000 Genomes Project, which was launched last month. The goal of the project is to sequence the genomes of at least 1,000 people from around the world to create the most detailed and medically useful picture to date of human genetic variation.

Ultimately, advances in bioinformatics will help push genetic science forward, shedding new light on human health and disease. Marth sees his lab’s role in providing critical tools that help researchers to organize data, interpret them, and visualize genome variations.

“We are excited to develop the software that will help these super-fast, high-throughput sequencing machines to realize their potential to produce invaluable data for research,” Marth said.

Nature Methods: http://www.nature.com/nmeth/journal/v5/n2/full/nmeth.1172.html.

The Marth research group: http://bioinformatics.bc.edu/marthlab/Main_Page.