Genome sequence of the olive tree, Olea europaea

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Metabarcoding Analysis of Fungal Diversity in the Phyllosphere and Carposphere of Olive (Olea europaea)

(2015) Ahmed Abdelfattah et al.   PLoS One

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species

(2014) Cene Gostinčar et al.   BMC GENOMICS

The Peculiar Landscape of Repetitive Sequences in the Olive (Olea europaea L.) Genome

(2014) Elena Barghini et al.   Genome Biology and Evolution

Comparative linkage maps suggest that fission, not polyploidy, underlies near-doubling of chromosome number within monkeyflowers (Mimulus; Phrymaceae)

(2014) L Fishman et al.   HEREDITY

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

(2013) Inanc Birol et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

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

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

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features

(2012) Hiroaki Iwata et al.   NUCLEIC ACIDS RESEARCH

Comparative Transcriptome Analysis of Two Olive Cultivars in Response to NaCl-Stress

(2012) Christos Bazakos et al.   PLoS One

Genetic Responses Induced in Olive Roots upon Colonization by the Biocontrol Endophytic Bacterium Pseudomonas fluorescens PICF7

(2012) Elisabetta Schilirò et al.   PLoS One

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

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

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Computational annotation of genes differentially expressed along olive fruit development

(2009) Giulio Galla et al.   BMC PLANT BIOLOGY

ABySS: A parallel assembler for short read sequence data

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

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY