Microsatellites Track Settings
 
Microsatellite repeats   (All Mapping and Sequencing tracks)

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Type of graph:
Track height: pixels (range: 11 to 128)
Data view scaling: Always include zero: 
Vertical viewing range: min:  max:   (range: 0 to 127)
Transform function:Transform data points by: 
Windowing function: Smoothing window:  pixels
Negate values:
Draw y indicator lines:at y = 0.0:    at y =
Graph configuration help
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 Configure 		 GA Microsatellites  GA Microsatellite repeats   Data format 
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 Configure 		 TC Microsatellites  TC Microsatellite repeats   Data format 
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 Configure 		 GC Microsatellites  GC Microsatellite repeats   Data format 
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 Configure 		 AT Microsatellites  AT Microsatellite repeats   Data format 
Data schema/format description and download
Assembly: Human Jan. 2022 (T2T CHM13v2.0/hs1)

Description

This track represents % of simple-sequence (2-mer) repeat pattern. Sequences composed of GA/TC/GC/AT bases are counted if one of the bases repeats (e.g. AAAATTTTAAATT are counted as 13 ATs). Patterns are obtained from every non-verlapping 128 bp window. Values displayed are the % of bases forming the specific repeat type, with a maximum value of 100. These sequence patterns are useful for predicting HiFi or ONT coverage biases, as described in Nurk et al. 2022 (Fig. 3) and Mc Cartney et al., 2022.

Display Conventions and Configuration

  •     - GA
  •     - TC
  •     - GC
  •     - AT

Methods

The track was generated using Seqrequester, a Meryl and Canu utility module. The tracks can be generated using seqrequester microsatellite. The code to generate these patterns can be found at T2T-Polish/pattern.

Release history

  • 2021/05/24, Microsatellite tracks for chm13.v1.0 assembly.
  • 2021/10/13, Microsatellite tracks for chm13.v1.1 assembly.
  • 2022/03/29, Microsatellite tracks for chm13.v2.0 assembly.

Credits

For inquiries, please contact us at Seqrequester or T2T-Polish.

References

  1. Nurk S, Koren S, Rhie A, Rautiainen M et al. The complete sequence of a human genome. Science (2022) doi: 10.1126/science.abj6987
  2. Mc Cartney AM, Shafin K, Alonge M et al. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. Nat. Methods (2022) doi: 10.1038/s41592-022-01440-3