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Researchers develop tool to evaluate genome sequencing method
Date:1/2/2013

of another kind. For instance, it shows how aggressively a genome assembler might have tried to pull together a group of genes into a contiguous piece of the genome, while incorrectly rearranging their correct order and copy numbers.

However, FRCurve has a significant limitationit can only gauge the accuracy of certain kinds of assemblers at one time, thereby excluding comparisons among the range of sequencing methods currently being employed. Many of these methods, where the original FRCurve failed, are becoming highly popular, as they are specifically designed to work with the most established next-generation sequencing technologies and are able to perform some error correction and data compression. However, by doing so, they also discard the original signature of key statistical features (e.g., position and orientation of the reads used to generate the candidate sequence) that FRCurve needs for evaluation.

The work reported in PLOS ONE unveils a new method, FRCbam, which has the capability to evaluate a much wider class of assemblers. It does so by reverse engineering the latent structures that were obscured by error-correction and data compression; and it performs this operation rapidly by using efficient and scalable mapping algorithms.

Instead of assumption-ridden simulation or expensive auxiliary methods, FRCbam validates its analysis by examining a large ensemble of assemblers working on a large ensemble of genomes, selected from crowd-sourced competitions like GAGE and Assemblathons. This way, FRCbam can characterize the statistics that are expected and then validate any individual system with respect to it.

FRCbam and FRCurve are expected to be used routinely to rank and evaluate future genome projects. This method is currently employed to evaluate the sequence assembly of the Norway Spruce, one of the largest genomes sequenced so farit is seven times longer than the human genome.


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Contact: James Devitt
james.devitt@nyu.edu
212-998-6808
New York University
Source:Eurekalert

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