A comparative analysis of methods for de novo assembly of hymenopteran genomes using either haploid or diploid samples

An integrative approach to untangling species delimitation in the Cataglyphis bicolor desert ant complex in Israel

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The Theory and Practice of Genome Sequence Assembly

(2015) Jared T. Simpson et al.   Annual Review of Genomics and Human Genetics

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine

(2015) Christine G. Elsik et al.   NUCLEIC ACIDS RESEARCH

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Caste-specific RNA editomes in the leaf-cutting ant Acromyrmex echinatior

(2014) Qiye Li et al.   Nature Communications

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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

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

Analysis of the bread wheat genome using whole-genome shotgun sequencing

(2012) Rachel Brenchley et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

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

(2012) Ruibang Luo et al.   GigaScience

The genome of the leaf-cutting antAcromyrmex echinatiorsuggests key adaptations to advanced social life and fungus farming

(2011) Sanne Nygaard et al.   GENOME RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The genome of the fire ant Solenopsis invicta

(2011) Y. Wurm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modernizing Reference Genome Assemblies

(2011) Deanna M. Church et al.   PLOS BIOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Mating system and population structure in the desert ant Cataglyphis livida

(2009) Iris Timmermans et al.   INSECTES SOCIAUX

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE