# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "DEploid" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'DEploid: Deconvolute Mixed Genomes with Unknown Proportions'
version: 0.5.3
doi: 10.1101/099499
abstract: Traditional phasing programs are limited to diploid organisms. Our method
  modifies Li and Stephens algorithm with Markov chain Monte Carlo (MCMC) approaches,
  and builds a generic framework that allows haplotype searches in a multiple infection
  setting. This package is primarily developed as part of the Pf3k project, which
  is a global collaboration using the latest sequencing technologies to provide a
  high-resolution view of natural variation in the malaria parasite Plasmodium falciparum.
  Parasite DNA are extracted from patient blood sample, which often contains more
  than one parasite strain, with unknown proportions. This package is used for deconvoluting
  mixed haplotypes, and reporting the mixture proportions from each sample.
authors:
- family-names: Zhu
  given-names: Joe
  email: sha.joe.zhu@gmail.com
- family-names: Almagro-Garcia
  given-names: Jacob
- family-names: McVean
  given-names: Gil
preferred-citation:
  type: article
  title: Deconvoluting multiple infections in \emphPlasmodium falciparum from high
    throughput sequencing data
  authors:
  - name: Sha Joe Zhu
  - name: Jacob Almagro-Garcia
  - name: Gil McVean
  year: '2017'
  journal: bioRxiv
  doi: 10.1101/099499
  publisher:
    name: Cold Spring Harbor Labs Journals
  url: http://www.biorxiv.org/content/early/2017/01/10/099499
repository: https://plasmogenepi.r-universe.dev
repository-code: https://github.com/DEploid-dev/DEploid-r
url: https://github.com/DEploid-dev/DEploid-r
date-released: '2020-04-21'
contact:
- family-names: Zhu
  given-names: Joe
  email: sha.joe.zhu@gmail.com