Draft genomes of two Atlantic bay scallop subspecies Argopecten irradians irradians and A. i. concentricus

Selection of a new scallop strain, QN‐2, from the backcross of Peruvian scallop × bay scallop F 1 hybrids with bay scallops

(2019) Dongxue Xu et al.   AQUACULTURE RESEARCH

Draft genome of the Peruvian scallop Argopecten purpuratus

(2018) Chao Li et al.   GigaScience

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

(2017) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

(2017) Jin Sun et al.   Nature Ecology & Evolution

Scallop genome provides insights into evolution of bilaterian karyotype and development

(2017) Shi Wang et al.   Nature Ecology & Evolution

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

(2014) Rei Kajitani et al.   GENOME RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Draft Genome of the Pearl Oyster Pinctada fucata: A Platform for Understanding Bivalve Biology

(2012) T. Takeuchi et al.   DNA RESEARCH

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

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

Introduction of the Peruvian scallop and its hybridization with the bay scallop in China

(2010) Chunde Wang et al.   AQUACULTURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TEclass--a tool for automated classification of unknown eukaryotic transposable elements

(2009) G. Abrusan et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

Database resources of the National Center for Biotechnology Information

(2009) Eric W. Sayers et al.   NUCLEIC ACIDS RESEARCH