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GSER (a Genome Size Estimator using R): a pipeline for quality assessment of sequenced genome libraries through genome size estimation. | LitMetric
The first step in any genome research after obtaining the read data is to perform a due quality control of the sequenced reads. In a genome assembly project, the second step is to estimate two important features, the genome size and 'best -mer', to start the assembly tests with different assembly software and its parameters. However, the quality control of the sequenced genome libraries as a whole, instead of focusing on the reads only, is frequently overlooked and realized to be important only when the assembly tests did not render the expected results. We have developed GSER, a Genome Size Estimator using R, a pipeline to evaluate the relationship between -mers and genome size, as a means for quality assessment of the sequenced genome libraries. GSER generates a set of charts that allow the analyst to evaluate the library datasets before starting the assembly. The script which runs the pipeline can be downloaded from http://www.mobilomics.org/GSER/downloads or http://github.com/mobilomics/GSER.
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