Redundans: an assembly pipeline for highly heterozygous genomes

The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis

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

Genome Comparison of Candida orthopsilosis Clinical Strains Reveals the Existence of Hybrids between Two Distinct Subspecies

(2014) Leszek P. Pryszcz et al.   Genome Biology and Evolution

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Comprehensive variation discovery in single human genomes

(2014) Neil I Weisenfeld et al.   NATURE GENETICS

Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana

(2014) Florian Maumus et al.   Nature Communications

Rapid Mechanisms for Generating Genome Diversity: Whole Ploidy Shifts, Aneuploidy, and Loss of Heterozygosity

(2014) R. J. Bennett et al.   Cold Spring Harbor Perspectives in Medicine

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

Parameters for accurate genome alignment

(2012) Martin C Frith et al.   BMC BIOINFORMATICS

GemSIM: general, error-model based simulator of next-generation sequencing data

(2012) Kerensa E McElroy et al.   BMC GENOMICS

Draft Genome Sequence of Wickerhamomyces ciferrii NRRL Y-1031 F-60-10

(2012) Jessica Schneider et al.   EUKARYOTIC CELL

HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies

(2012) S. Huang et al.   GENOME RESEARCH

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Evolutionary Role of Interspecies Hybridization and Genetic Exchanges in Yeasts

(2012) Lucia Morales et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler

(2009) Daniel R. Zerbino et al.   PLoS One

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY