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RPGG construction

TL Tsung-Yu Lu
PS Paulina N. Smaruj
GF Geoffrey Fudenberg
NM Nicholas Mancuso
MC Mark J.P. Chaisson
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A set of 88,441 VNTR coordinates was retrieved from danbing-tk v1.3 (Lu et al. 2021). The VNTR set was obtained by (1) detecting VNTRs over the five haplotype-resolved assemblies (AK1, HG00514, HG00733, NA19240, NA24385) released by Lu et al. (2021) using Tandem Repeat Finder v4.09.1 (Benson 1999), (2) selecting for VNTRs with a size between 100 bp and 10 kbp and a motif size > 6 bp, and (3) applying danbing-tk to the VNTRs in the five genomes to identify 88,441 loci with proper orthology mapping. VNTR annotations on the 35 HGSVC assemblies and the corresponding RPGG were generated using the build module of danbing-tk, giving a total of 80,518 loci.

Copyright and License information:  ©2023
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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