XYalign: Inferring and Correcting for Sex Chromosome Ploidy in Next-Generation Sequencing Data

Authors:Timothy Webster, Madeline Couse, Bruno Grande, Eric Karlins, Tanya Phung, Phillip Richmond, Whitney Whitford, Melissa Wilson Sayres Date:Apr 11, 2019 Release:1.1.6 Download:Github Repository Forum/Mailing List:  Google Group Issues:Please submit any bugs, problems, or feature requests as issues via Github

The high degree of similarity between gametologous sequences on the sex chromosomes can lead to the misalignment of sequencing reads and substantially affect variant calling. Here we present XYalign, a new tool that (1) aids in the inference of sex chromosome content using NGS data, (2) remaps reads based on the inferred sex chromosome complement of the individual, and (3) outputs quality, depth, and allele-balance metrics across chromosomes.

Contents:

• Installation
  • Operating System
  • Requirements
  • Obtaining XYalign
  • Pip
• Usage Overview
  • The Basics
  • Recommendations for Incorporating XYalign into Pipelines
  • XYalign - Speed and Memory
  • Exome data
  • Nonhuman genomes
  • Analyzing arbitrary chromosomes
  • Using XYalign as a Python library
  • Full List of Command-Line Flags
• Frequently Asked Questions
  • Does XYalign require X and Y chromosomes?
  • Will XYalign work with genomes from other organisms?
• API
  • xyalign
  • xyalign package
  • xyalign.assemble module
  • xyalign.bam module
  • xyalign.ploidy module
  • xyalign.reftools module
  • xyalign.utils module
  • xyalign.variants module
  • xyalign.xyalign module
• Release History
  • 1.1.6
  • 1.1.5
  • 1.1.3
  • 1.1.2
  • 1.1.1
  • 1.1.0
  • 1.0.0
  • 0.1.1
  • 0.1.0
  • 0.0.1 Prerelease

Indices and tables

• Index
• Module Index
• Search Page