SEDEF Segmental Dups Track Settings
SEDEF Segmental Duplications   (All Variation and Repeats tracks)

Display mode:   

Show only items with score at or above:   (range: 0 to 1000)

Display data as a density graph:

Data schema/format description and download


A track showing segmental duplications as generated by sedef on the assembly: T2T-CHM13-v2.0 Column descriptions can be found here: columns.

Display Conventions and Configuration

This section describes track configuration controls, or any special display conventions such as the meaning of different colors in your tracks.

The colours used for level of similary segmentation standard:

less than 90% similarityPurple
90 - 98% similarityLight to dark gray
98 - 99% similarityYellow
greater than 99% similarityOrange


Sedef was run with default parameters on a RepeatMasked genome assembly. The resulting output (final.bed) was then converted into a browser friendly format (bed9 + extra fields).



M. R. Vollger et al., Segmental duplications and their variation in a complete human genome. Science. 2022 April 1; eabj6965. DOI: 10.1126/science.abj6965

Numanagic I, Gökkaya AS, Zhang L, Berger B, Alkan C, Hach F. Fast characterization of segmental duplications in genome assemblies. Bioinformatics. 2018 Sep 1;34(17):i706-i714. PMID: 30423092; PMC: PMC6129265