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Published May 13, 2021 | Version v0.3.2
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Comparative Genomic Read Depth for Studying Genomic Copy Number Variation

  • 1. Kansas State University

Description

CGRD is a pipeline to compare sequencing read depths from two samples along a reference genome. Three major steps include:

  1. define effective genomic bins each of which harbors certain non-repetitive sequences
  2. align reads and count read depths per bin for both samples
  3. combine neighboring bins with similar fold changes in read depth between the two samples (segmentation)

From the result, genomic segments with similar and differential (higher or lower) read depths are obtained. Therefore, genomic copy number variation (CNV) based on read depths can be extracted from the result and visualized on the genome map.

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CGRD.zip

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Additional details

Funding

ECA-PGR: Under the Hood: The Genetic Components of Maize Transformation 1741090
National Science Foundation