De novo genome assembly evaluation

Probabilistic measure of assembly quality

LAP is a de novo probabilistic measure of assembly quality which allows an objective comparison of multiple assemblies generated from a same set of reads. Specifically, we define the quality of an assembly as the conditional probability of the sequenced reads given the sequence output by the assembler, value maximized by the true genome sequence.

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Latest Release

LAP 1.1	9/3/13
Please cite: Ghodsi, M., Hill, C. M., Astrovskaya, I., Lin, H., Sommer, D. D., Koren, S., & Pop, M. De novo likelihood-based measures for comparing genome assemblies." BMC research notes 6 (2013): 334.

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Authors

Mohammadreza Ghodsi
Christopher Hill
Irina Astrovskaya
Henry Lin
Dan Sommer
Sergey Koren
Mihai Pop

Other Documentation

OMICS Day, 5/12 (.pdf)

Links

September 3rd, 2013

Added -n parameter to allow comparison of metagenomic assemblies.

April 15, 2013

Updated Getting started.
Fixed issue with creating ./tmp and ./indexes directories.

December 17, 2012

Website created.