Genome sequence of pacific abalone (Haliotis discus hannai): the first draft genome in family Haliotidae
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Appeltans, 2012, World Register of Marine Species
Hamer, 2010, Understanding the ecological role of abalone in the reef ecosystem of Victoria, Fish Res Rep
Elliott, 2000, Genetic improvement programmes in abalone: what is the future?, Aqua Res, 31, 51, 10.1046/j.1365-2109.2000.00386.x
Gordon, 2004, World abalone fisheries and aquaculture update: supply and market dynamics, J Shellfish Res, 23, 935
Suleria, 2015, Therapeutic potential of abalone and status of bioactive molecules: a comprehensive review, Crit Rev Food Sci Nutr, 57, 1742, 10.1080/10408398.2015.1031726
Lim, 2014, Cytotoxic and antioxidant activities of abalone (Haliotis discus hannai) extracts, J Life Sci, 24, 737, 10.5352/JLS.2014.24.7.737
Lee, 2010, Abalone visceral extract inhibit tumor growth and metastasis by modulating Cox-2 levels and CD8+ T cell activity, BMC Complement Alt Med, 10, 1
Andrews, 2014, FastQC a quality-control tool for high-throughput sequence data
Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, btu170
O’Connell, 2015, NxTrim: optimized trimming of Illumina mate pair reads, Bioinformatics, 31, 2035, 10.1093/bioinformatics/btv057
Marçais, 2011, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, 27, 764, 10.1093/bioinformatics/btr011
Boetzer, 2011, Scaffolding pre-assembled contigs using SSPACE, Bioinformatics, 27, 578, 10.1093/bioinformatics/btq683
English, 2012, Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology, PloS One, 7, e47768, 10.1371/journal.pone.0047768
Luo, 2012, SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler, GigaScience, 1, 1, 10.1186/2047-217X-1-18
Tarailo‐ Graovac, 2009, Using RepeatMasker to identify repetitive elements in genomic sequences, Curr Protoc Bioinformatics, 10.1002/0471250953.bi0410s25
Jurka, 2005, Repbase Update, a database of eukaryotic repetitive elements, Cyt Genome Res, 110, 462, 10.1159/000084979
Bao, 2002, Automated de novo identification of repeat sequence families in sequenced genomes, Genome Res, 12, 1269, 10.1101/gr.88502
Price, 2005, De novo identification of repeat families in large genomes, Bioinformatics, 21, i351, 10.1093/bioinformatics/bti1018
Benson, 1999, Tandem repeats finder: a program to analyze DNA sequences, Nucleic Acids Res, 27, 573, 10.1093/nar/27.2.573
Bailly-Bechet, 2014, “One code to find them all”: a perl tool to conveniently parse RepeatMasker output files, Mobile DNA, 5, 1, 10.1186/1759-8753-5-13
Chénais, 2012, The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments, Gene, 509, 7, 10.1016/j.gene.2012.07.042
Kidwell, 2002, Transposable elements and the evolution of genome size in eukaryotes, Genetica, 115, 49, 10.1023/A:1016072014259
Trapnell, 2009, TopHat: discovering splice junctions with RNA-Seq, Bioinformatics, 25, 1105, 10.1093/bioinformatics/btp120
Trapnell, 2012, Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nat Protocols, 7, 562, 10.1038/nprot.2012.016
Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res, 25, 3389, 10.1093/nar/25.17.3389
Slater, 2005, Automated generation of heuristics for biological sequence comparison, BMC Bioinformatics, 6, 31, 10.1186/1471-2105-6-31
Stanke, 2008, Using native and syntenically mapped cDNA alignments to improve de novo gene finding, Bioinformatics, 24, 637, 10.1093/bioinformatics/btn013
Solovyev, 2006, Automatic annotation of eukaryotic genes, pseudogenes and promoters, Genome Biol, 7, S10, 10.1186/gb-2006-7-s1-s10
Blanco, 2007, Using geneid to identify genes, Curr Protoc Bioinformatics, 10.1002/0471250953.bi0403s18
Haas, 2008, Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments, Genome Biol, 9, R7, 10.1186/gb-2008-9-1-r7
Nam, 2017, Supporting data for “Genome sequence of pacific abalone (Haliotis discus hannai): the first draft genome in family Haliotidae” GigaScience Database