HaploTypo: a variant-calling pipeline for phased genomes

Gene flow contributes to diversification of the major fungal pathogen Candida albicans

(2018) Jeanne Ropars et al.   Nature Communications

Diverse Lineages of Candida albicans Live on Old Oaks

(2018) Douda Bensasson et al.   GENETICS

Hybridization and emergence of virulence in opportunistic human yeast pathogens

(2017) Verónica Mixão et al.   YEAST

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

(2016) Peter Edge et al.   GENOME RESEARCH

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Redundans: an assembly pipeline for highly heterozygous genomes

(2016) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

IDP-ASE: haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing

(2016) Benjamin Deonovic et al.   NUCLEIC ACIDS RESEARCH

ASEQ: fast allele-specific studies from next-generation sequencing data

(2015) Alessandro Romanel et al.   BMC Medical Genomics

dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes

(2015) Yana Safonova et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis

(2015) Leszek P. Pryszcz et al.   PLoS Genetics

WinHAP2: an extremely fast haplotype phasing program for long genotype sequences

(2014) Weihua Pan et al.   BMC BIOINFORMATICS

Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure

(2013) Dale Muzzey et al.   GENOME BIOLOGY

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH