#3 Napari-KICS

Demonstrator: Napari-KICS

Speaker: Arne Ludwig

Date: October 27th 2022, 1 p.m. – 2 p.m.

Location: APB-1020, Andreas-Pfitzmann-Bau (APB), Nöthnitzer Str. 46, Dresden

Know your chromosome sizes: a guide to karyotype-based validation of de novo assemblies.

Application: https://github.com/mpicbg-csbd/napari-kics

Impressions from our Hands-On Session on Napari-KICS.

Chromosome-scale genome assembly is affected by scaffolding errors and may yield incorrect chromosome sizes. Today, we present KICS, a semi-automated and cost-efficient approach for examining the validity of the assembly by estimating relative chromosome sizes from the respective karyotype images. The method employs threshold-based image segmentation and uses the extracted chromosome areas as proxies for the actual chromosome sizes. The suitability of the approach is confirmed by a strong correlation between area and DNA content evaluated on karyotype images of varied species and achieving a 6 Mb chromosome size error on a reference human karyotype dataset.

Find out more about our Hands-on Demonstrator Series!

TU
Universität
Max
Leibnitz-Institut
Helmholtz
Hemholtz
Institut
Fraunhofer-Institut
Fraunhofer-Institut
Max-Planck-Institut
Institute
Max-Plank-Institut