Summary sheet

Feature Description
Main use Inference of COI, proportions, haplotypes and within-sample IBD
Authors Sha Joe Zhu, Jacob Almargo-Garcia, Gil McVean
Latest version v0.6-beta
Website https://deploid.readthedocs.io/en/latest/index.html
Code repository https://github.com/DEploid-dev/DEploid
Publication https://doi.org/10.7554/eLife.40845 (DEploidIBD), https://doi.org/10.1093/bioinformatics/btx530 (DEploid)
Tutorial Author Jason A. Hendry
Tutorial Date 11-Dec-2023

Purpose

The main purpose of DEploidIBD is to infer complexity of infection (COI), strain proportions, strain haplotypes, and within-sample IBD from P. falciparum whole genome sequencing (WGS) data.

Existing resources

  • There is a github repository containing the source code. Note that both DEploid and DEploidIBD run from the same codebase, with the later being invoked when the -ibd flag is used.
  • There is also a website with additional information about installaion and running the tools.
  • For DEploid, some examples of how to run the software are available in the supplementary data.

Citation

If you run DEploidIBD, please use the following citation:

@article{RN96,
   author = {Zhu, Sha Joe and Hendry, Jason A. and Almagro-Garcia, Jacob and Pearson, Richard D. and Amato, Roberto and Miles, Alistair and Weiss, Daniel J. and Lucas, Tim C. D. and Nguyen, Michele and Gething, Peter W. and Kwiatkowski, Dominic and McVean, Gil},
   title = {The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria},
   journal = {eLife},
   volume = {8},
   pages = {e40845},
   ISSN = {2050-084X},
   DOI = {10.7554/eLife.40845},
   url = {https://doi.org/10.7554/eLife.40845},
   year = {2019},
   type = {Journal Article}
}

Or if you run DEploid, use:

@article{Zhu2018,
   author = {Zhu, S. J. and Almagro-Garcia, J. and McVean, G.},
   title = {Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data},
   journal = {Bioinformatics},
   volume = {34},
   number = {1},
   pages = {9-15},
   ISSN = {1367-4803 (Print)
1367-4803},
   DOI = {10.1093/bioinformatics/btx530},
   year = {2018},
   type = {Journal Article}
}
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