RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes
Tài liệu tham khảo
NCBI Resource Coordinators, 2018, Database resources of the national center for biotechnology information, Nucleic Acids Res, 46, D8, 10.1093/nar/gkx1095
Lander, 2001, Initial sequencing and analysis of the human genome, Nature, 409, 860, 10.1038/35057062
Shendure, 2008, Next-generation DNA sequencing, Nat Biotechnol, 26, 1135, 10.1038/nbt1486
Al-Mssallem, 2013, Genome sequence of the date palm Phoenix dactylifera L, Nat Commun, 4, 2274, 10.1038/ncomms3274
Xu, 2014, Genome sequence and genetic diversity of the common carp, Cyprinus carpio, Nat Genet, 46, 1212, 10.1038/ng.3098
Li, 2009, The sequence alignment/map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352
Li, 2011, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, 27, 2987, 10.1093/bioinformatics/btr509
Li, 2011, Improving SNP discovery by base alignment quality, Bioinformatics, 27, 1157, 10.1093/bioinformatics/btr076
McKenna, 2010, The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res, 20, 1297, 10.1101/gr.107524.110
Otto, 2011, RATT: rapid annotation transfer tool, Nucleic Acids Res, 39, e57, 10.1093/nar/gkq1268
Otto, 2010, Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology, Bioinformatics, 26, 1704, 10.1093/bioinformatics/btq269
Kent, 2002, The human genome browser at UCSC, Genome Res, 12, 996, 10.1101/gr.229102
Goecks, 2010, Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences, Genome Biol, 11, R86, 10.1186/gb-2010-11-8-r86
Blankenberg, 2010, Galaxy: a web-based genome analysis tool for experimentalists, Curr Protoc Mol Biol, 19, 19.10.1
Giardine, 2005, Galaxy: a platform for interactive large-scale genome analysis, Genome Res, 15, 1451, 10.1101/gr.4086505
Benson, 1999, Tandem repeats finder: a program to analyze DNA sequences, Nucleic Acids Res, 27, 573, 10.1093/nar/27.2.573
Wang, 2017, GSA: genome sequence archive, Genomics Proteomics Bioinformatics, 15, 14, 10.1016/j.gpb.2017.01.001
Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170
Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat Methods, 9, 357, 10.1038/nmeth.1923
Garrison, 2012, Haplotype-based variant detection from short-read sequencing, arXiv
Kent, 2002, BLAT—the BLAST-like alignment tool, Genome Res, 12, 656, 10.1101/gr.229202
Ling, 2014, VCGDB: a dynamic genome database of the Chinese population, BMC Genomics, 15, 1, 10.1186/1471-2164-15-265
Ruffier, 2017, Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation, Database (Oxford), 2017, bax020, 10.1093/database/bax020
Haas, 2003, Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies, Nucleic Acids Res, 31, 5654, 10.1093/nar/gkg770
Holt, 2011, MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects, Bioinformatics, 12, 1
Delcher, 2003, Using MUMmer to identify similar regions in large sequence sets, Curr Protoc Bioinformatics, 10, 3
Wang, 2010, ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data, Nucleic Acids Res, 38, e164, 10.1093/nar/gkq603