Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics’ GemCode Sequencing Data

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sealer: a scalable gap-closing application for finishing draft genomes

(2015) Daniel Paulino et al.   BMC BIOINFORMATICS

Konnector v2.0: pseudo-long reads from paired-end sequencing data

(2015) Benjamin P Vandervalk et al.   BMC Medical Genomics

Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation

(2015) Shaun D. Jackman et al.   Genome Biology and Evolution

Startups use short-read data to expand long-read sequencing market

(2015) Michael Eisenstein   NATURE BIOTECHNOLOGY

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism

(2015) René L. Warren et al.   PLANT JOURNAL

LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads

(2015) René L. Warren et al.   GigaScience

BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters

(2014) Justin Chu et al.   BIOINFORMATICS

Insights into Conifer Giga-Genomes

(2014) A. R. De La Torre et al.   PLANT PHYSIOLOGY

An Improved Protocol for Intact Chloroplasts and cpDNA Isolation in Conifers

(2014) Leila do Nascimento Vieira et al.   PLoS One

Fine-scale environmental variation contributes to introgression in a three-species spruce hybrid complex

(2014) Jill A. Hamilton et al.   Tree Genetics & Genomes

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Unbiased estimation of chloroplast number in mesophyll cells: advantage of a genuine three-dimensional approach

(2013) Zuzana Kubínová et al.   JOURNAL OF EXPERIMENTAL BOTANY

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

An integrated genomic, proteomic and biochemical analysis of (+)-3-carene biosynthesis in Sitka spruce (Picea sitchensis) genotypes that are resistant or susceptible to white pine weevil

(2010) Dawn E. Hall et al.   PLANT JOURNAL

ABySS: A parallel assembler for short read sequence data

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

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

(2008) Richard Cronn et al.   NUCLEIC ACIDS RESEARCH