Genomic Next-generation Universal MAPper (gnumap)

Overview: The Genomic Next-generation Universal MAPper (gnumap) is a program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. Currently, gnumap is designed to be used with the _int.txt data received from the Solexa/Illumina machine.

With the emergence of high-throughput next-generation sequencing machines, an incredible amount of data is being produced at a very high rate. The big problem is mapping this data back to the genome. One significant problem with many genomic mapping programs is the way duplicate regions in genomic DNA are dealt with. Since it is impossible to know where exactly where a duplicate region should be mapped to, many programs simply throw out these sequences. Often, this results in a loss of nearly 40% of the data.

This project develops gnumap, a program capable of handling such repetitive regions. By using statistical formulas, we are able to account for these repetitive reads by distributing them across several regions in the genome. In addition, the output of the program is created in such a way that it can be easily viewed through other free and readily-available programs. Several benchmark data sets were created with spiked-in duplicate regions, and gnumap was able to more accurately account for these duplicate regions.

GNUMAP Users Google Group

• If you would like to become a part of the google group, send questions to the group as a whole, or browse questions that have been asked previously, please visit here.

News

• GNUMAP can now save and read in a binary genome file! The latest version is available here.
• The GNUMAP algorithm and results have been presented several places, including ISMB 2009 in Stockholm, Sweden.
  The presentation can be downloaded as a pptx or pdf.

Recent Updates:

• As of 28 May, 2009, GNUMAP has added many features in order to enable methylation analysis, including allowing for c->t or a->g transitions. For questions or directions please email Nathan at nathanlclement (at) gmail.com.