ArticleBioinformatics (Oxford, England)2020
HaploTypo: a variant-calling pipeline for phased genomes.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Hybrids unleashed: exploring the emergence and genomic insights of pathogenic yeast hybrids.Current opinion in microbiology · 2024Review
- Origin of fungal hybrids with pathogenic potential from warm seawater environments.Nature communications · 2023Article
- Lipid A Modification and Metabolic Adaptation in Polymyxin-Resistant, New Delhi Metallo-β-Lactamase-Producing Klebsiella pneumoniae.Microbiology spectrum · 2023Article
- Article
- Evolution of loss of heterozygosity patterns in hybrid genomes of Candida yeast pathogens.BMC biology · 2023Article
- Article
- Genome analysis of Candida subhashii reveals its hybrid nature and dual mitochondrial genome conformations.DNA research : an international journal for rapid publication of reports on genes and genomes · 2021Article
- Extreme diversification driven by parallel events of massive loss of heterozygosity in the hybrid lineage of Candida albicans.Genetics · 2021Article
- Factors enforcing the species boundary between the human pathogens Cryptococcus neoformans and Cryptococcus deneoformans.PLoS genetics · 2021Article
- The Transcriptional Aftermath in Two Independently Formed Hybrids of the Opportunistic Pathogen Candida orthopsilosis.mSphere · 2020Article
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5 authors.
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Abstract
summaryAn increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, the most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve haplotypes in genetic variation analyses. HaploTypo infers the haplotype correspondence for each heterozygous variant called on a phased reference genome. AVAILABILITY AND IMPLEMENTATION: HaploTypo is implemented in Python 2.7 and Python 3.5, and is freely available at https://github.com/gabaldonlab/haplotypo, and as a Docker image. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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