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Haplotype-resolved genome of heterozygous African cassava TMEB117 (Manihot esculenta)

This repository contains scripts of the methodology for assembling the genome of the TMEB117 cassava cultivar. Utilizing PacBio HiFi reads, we constructed a haplotype-resolved genome with an accuracy of QV > 64, N50 > 35 Mbp, and 98.9% BUSCO completeness. This represents the most precise cassava genome sequence to date. The genome is characterized by heterozygosity, encompassing over 60% repetitive elements. Our gene prediction identified more than 45,000 gene models for both haplotypes.

Scripts for methodology section

  • BashScripts
    • QC_to_Assembly.sh: Bash commands covering quality control to genome assembly.
    • annotation.sh: Commands for transposable elements (TE) and the funannotate singularity script used in the gene annotation section.
  • R scripts: scripts for TE and gene annotation visualizations

For more details and methods, please take a look at the published paper [here](link provided soon).