In2lt inversion status and de novo assembly of a wild-derived Drosophila melanogaster

Date: May 21st, 2024

This repository hosts the scripts utilized for generating a de novo assembly of Drosophila melanogaster.

Author:

Connor S. Murray
Email: csm6hg@virginia.edu

Script Repository:

cnv_analysis:

Contains the scripts used for classifying structural variants (SVs) across NGS data.

• Smoove:
  • Smoove used to call SVs across short-read dataset.

DeNovoAssembly:

Contains associated scripts for de novo assembly of PacBio HiFi reads, scaffolding, and dotplot creation.

• HiCanu:

  • De novo assembly software.

• LongStitch:

  • Scaffolding of contigs software.

• BUSCO:

  • Benchmark universal single-copy orthologous (BUSCO) genes to assess genome completeness.

• Dotplot_DGenies:

  • DGenies used to compare sequences with DMel6 genome.