Regional sequence expansion or collapse in heterozygous genome assemblies

The genome of a subterrestrial nematode reveals adaptations to heat

(2019) Deborah J. Weinstein et al.   Nature Communications

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Assembly and RNA-free annotation of highly heterozygous genomes: The case of the thick-billed murre (Uria lomvia )

(2017) Anna Tigano et al.   Molecular Ecology Resources

Redundans: an assembly pipeline for highly heterozygous genomes

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

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Genetic variation and the de novo assembly of human genomes

(2015) Mark J. P. Chaisson et al.   NATURE REVIEWS GENETICS

Omega: an Overlap-graph de novo Assembler for Metagenomics

(2014) Bahlul Haider et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Rei Kajitani et al.   GENOME RESEARCH

Space-efficient and exact de Bruijn graph representation based on a Bloom filter

(2013) Rayan Chikhi et al.   Algorithms for Molecular Biology

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Sequence assembly demystified

(2013) Niranjan Nagarajan et al.   NATURE REVIEWS GENETICS

Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly

(2013) Yen-Chun Chen et al.   PLoS One

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Parameters for accurate genome alignment

(2012) Martin C Frith et al.   BMC BIOINFORMATICS

A survey of error-correction methods for next-generation sequencing

(2012) X. Yang et al.   BRIEFINGS IN BIOINFORMATICS

Finished bacterial genomes from shotgun sequence data

(2012) F. J. Ribeiro 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

De novo genome assembly: what every biologist should know

(2012) Monya Baker   NATURE METHODS

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Ruibang Luo et al.   GigaScience

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

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

(2011) H. Li   BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Sequencing technologies and genome sequencing

(2011) Chandra Shekhar Pareek et al.   JOURNAL OF APPLIED GENETICS

Nematoda from the terrestrial deep subsurface of South Africa

(2011) G. Borgonie et al.   NATURE

Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

(2010) Sébastien Boisvert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

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

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Applications of next-generation sequencing technologies in functional genomics

(2008) Olena Morozova et al.   GENOMICS

Genome assembly forensics: finding the elusive mis-assembly

(2008) Adam M Phillippy et al.   GENOME BIOLOGY