Hawkeye: Finally a tool for assembly validation!

This is related to my first posting. Mike Schatz, a very talented graduate student in Computer Sciences at The University of Maryland College Park Center for Bioinformatics and Computional Biology (CBCB) working with Steven Salzberg, has published today a really good paper entitled "Hawkeye: a visual analytics tool for genome assemblies" in Genome Biology. Finally a tool that allows any scientist to evaluate the quality of a genome assembly. The paper describes the capabilities of the software, including assembly vizualization (including traces), assembly analysis (assembly statistics), contig viewer and scaffold viewer among others. The software is amazingly fast and doesn't slow down when working with large genomes and allows for assembly problems diagnotics and validation. Mike even describes how Hawkeye can be use for biological investigation. Using Hawkeye, Mike was able to identify the assembly of the 6 plasmids harbored by Bacillus megaterium one of my project.

I think this software should become a standard which reviewers, editors... could use to validate genome assemblies prior to publication. Now, all we need is the genome sequencing scientific community to agree on data release standards, more than the consensus sequence will be needed!

This paper is published as "Open Access" and Hawkeye is freely available as part of the AMOS package on sourceforge. Steven Salzberg's group published another paper in the same issue of Genome Biology on "computional discovery of Rho-independant trasncription terminators" as well as a very interesting editorial on "Genome re-annotation: a wiki solution?", unfortunately not as Open Access.

One more thing, Hawkeye works on a Mac. A huge plus to me!!

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