Gritsenko AA, Nijkamp JF, Reinders MJ, de Ridder D: GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies. Bioinformatics. 2012, 28 (11): 1429-1437. 10.1093/bioinformatics/bts175.

Article
CAS
PubMed
Google Scholar

Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W: Scaffolding pre-assembled contigs using SSPACE. Bioinformatics. 2011, 27 (4): 578-579. 10.1093/bioinformatics/btq683.

Article
CAS
PubMed
Google Scholar

Gao S, Sung WK, Nagarajan N: Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. J Comput Biol. 2011, 18 (11): 1681-1691. 10.1089/cmb.2011.0170.

Article
PubMed Central
CAS
PubMed
Google Scholar

Salmela L, Makinen V, Valimaki N, Ylinen J, Ukkonen E: Fast scaffolding with small independent mixed integer programs. Bioinformatics. 2011, 27 (23): 3259-3265. 10.1093/bioinformatics/btr562.

Article
PubMed Central
CAS
PubMed
Google Scholar

Gordon D, Abajian C, Green P: Consed: a graphical tool for sequence finishing. Genome Res. 1998, 8 (3): 195-202.

Article
CAS
PubMed
Google Scholar

Burland TG: DNASTAR’s Lasergene sequence analysis software. Methods Mol Biol. 2000, 132: 71-91.

CAS
PubMed
Google Scholar

Bonfield JK, Smith K, Staden R: A new DNA sequence assembly program. Nucleic Acids Res. 1995, 23 (24): 4992-4999. 10.1093/nar/23.24.4992.

Article
PubMed Central
CAS
PubMed
Google Scholar

Nielsen CB, Cantor M, Dubchak I, Gordon D, Wang T: Visualizing genomes: techniques and challenges. Nat Methods. 2010, 7 (3 Suppl): S5-S15.

Article
CAS
PubMed
Google Scholar

Nielsen CB, Jackman SD, Birol I, Jones SJ: ABySS-Explorer: visualizing genome sequence assemblies. IEEE Trans Vis Comput Graph. 2009, 15 (6): 881-888.

Article
PubMed
Google Scholar

Riba-Grognuz O, Keller L, Falquet L, Xenarios I, Wurm Y: Visualization and quality assessment of de novo genome assemblies. Bioinformatics. 2011, 27 (24): 3425-3426. 10.1093/bioinformatics/btr569.

Article
CAS
PubMed
Google Scholar

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13 (11): 2498-2504. 10.1101/gr.1239303.

Article
PubMed Central
CAS
PubMed
Google Scholar

Bonfield JK, Whitwham A: Gap5–editing the billion fragment sequence assembly. Bioinformatics. 2010, 26 (14): 1699-1703. 10.1093/bioinformatics/btq268.

Article
PubMed Central
CAS
PubMed
Google Scholar

Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D: The human genome browser at UCSC. Genome Res. 2002, 12 (6): 996-1006.

Article
PubMed Central
CAS
PubMed
Google Scholar

Stalker J, Gibbins B, Meidl P, Smith J, Spooner W, Hotz HR, Cox AV: The Ensembl Web site: mechanics of a genome browser. Genome Res. 2004, 14 (5): 951-955. 10.1101/gr.1863004.

Article
PubMed Central
CAS
PubMed
Google Scholar

Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP: Integrative genomics viewer. Nat Biotechnol. 2011, 29 (1): 24-26. 10.1038/nbt.1754.

Article
PubMed Central
CAS
PubMed
Google Scholar

Huang W, Marth G: EagleView: a genome assembly viewer for next-generation sequencing technologies. Genome Res. 2008, 18 (9): 1538-1543. 10.1101/gr.076067.108.

Article
PubMed Central
CAS
PubMed
Google Scholar

Schatz MC, Phillippy AM, Shneiderman B, Salzberg SL: Hawkeye: an interactive visual analytics tool for genome assemblies. Genome Biol. 2007, 8 (3): R34-10.1186/gb-2007-8-3-r34.

Article
PubMed Central
PubMed
Google Scholar

Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25 (14): 1754-1760. 10.1093/bioinformatics/btp324.

Article
PubMed Central
CAS
PubMed
Google Scholar

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The sequence alignment/Map format and SAMtools. Bioinformatics. 2009, 25 (16): 2078-2079. 10.1093/bioinformatics/btp352.

Article
PubMed Central
PubMed
Google Scholar

Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010, 26 (6): 841-842. 10.1093/bioinformatics/btq033.

Article
PubMed Central
CAS
PubMed
Google Scholar

Tang B, Zhao W, Zheng H, Zhuo Y, Zhang L, Zhao GP: Complete genome sequence of Amycolatopsis mediterranei S699 based on de novo assembly via a combinatorial sequencing strategy. J Bacteriol. 2012, 194 (20): 5699-5700. 10.1128/JB.01295-12.

Article
PubMed Central
CAS
PubMed
Google Scholar

Xu J, Zheng HJ, Liu L, Pan ZC, Prior P, Tang B, Xu JS, Zhang H, Tian Q, Zhang LQ: Complete genome sequence of the plant pathogen Ralstonia solanacearum strain Po82. J Bacteriol. 2011, 193 (16): 4261-4262. 10.1128/JB.05384-11.

Article
PubMed Central
CAS
PubMed
Google Scholar

Mi S, Song J, Lin J, Che Y, Zheng H: Complete genome of Leptospirillum ferriphilum ML-04 provides insight into its physiology and environmental adaptation. J Microbiol. 2011, 49 (6): 890-901. 10.1007/s12275-011-1099-9.

Article
CAS
PubMed
Google Scholar

He J, Shao X, Zheng H, Li M, Wang J, Zhang Q, Li L, Liu Z, Sun M, Wang S: Complete genome sequence of Bacillus thuringiensis mutant strain BMB171. J Bacteriol. 2010, 192 (15): 4074-4075. 10.1128/JB.00562-10.

Article
PubMed Central
CAS
PubMed
Google Scholar

Yang M, Lv Y, Xiao J, Wu H, Zheng H, Liu Q, Zhang Y, Wang Q: Edwardsiella comparative phylogenomics reveal the new intra/inter-species taxonomic relationships, virulence evolution and niche adaptation mechanisms. PLoS One. 2012, 7 (5): e36987-10.1371/journal.pone.0036987.

Article
PubMed Central
CAS
PubMed
Google Scholar

You XY, Liu C, Wang SY, Jiang CY, Shah SA, Prangishvili D, She Q, Liu SJ, Garrett RA: Genomic analysis of Acidianus hospitalis W1 a host for studying crenarchaeal virus and plasmid life cycles. Extremophiles. 2011, 15 (4): 487-497. 10.1007/s00792-011-0379-y.

Article
PubMed Central
CAS
PubMed
Google Scholar

Chen YF, Gao F, Ye XQ, Wei SJ, Shi M, Zheng HJ, Chen XX: Deep sequencing of Cotesia vestalis bracovirus reveals the complexity of a polydnavirus genome. Virology. 2011, 414 (1): 42-50. 10.1016/j.virol.2011.03.009.

Article
CAS
PubMed
Google Scholar

Li Y, Zheng H, Liu Y, Jiang Y, Xin J, Chen W, Song Z: The complete genome sequence of Mycoplasma bovis strain Hubei-1. PLoS One. 2011, 6 (6): e20999-10.1371/journal.pone.0020999.

Article
PubMed Central
CAS
PubMed
Google Scholar

Zheng P, Xia Y, Xiao G, Xiong C, Hu X, Zhang S, Zheng H, Huang Y, Zhou Y, Wang S: Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional Chinese medicine. Genome Biol. 2011, 12 (11): R116-10.1186/gb-2011-12-11-r116.

Article
PubMed Central
CAS
PubMed
Google Scholar

Assenov Y, Ramirez F, Schelhorn SE, Lengauer T, Albrecht M: Computing topological parameters of biological networks. Bioinformatics. 2008, 24 (2): 282-284. 10.1093/bioinformatics/btm554.

Article
CAS
PubMed
Google Scholar

Pop M, Phillippy A, Delcher AL, Salzberg SL: Comparative genome assembly. Brief Bioinform. 2004, 5 (3): 237-248. 10.1093/bib/5.3.237.

Article
CAS
PubMed
Google Scholar

Verma M, Kaur J, Kumar M, Kumari K, Saxena A, Anand S, Nigam A, Ravi V, Raghuvanshi S, Khurana P: Whole genome sequence of the rifamycin B-producing strain Amycolatopsis mediterranei S699. J Bacteriol. 2011, 193 (19): 5562-5563. 10.1128/JB.05819-11.

Article
PubMed Central
CAS
PubMed
Google Scholar

Gordon D: Viewing and editing assembled sequences using consed. Curr Protoc Bioinformatics. 2003, Chapter 11 (Unit11): 12-

Google Scholar

Gordon D: Automated finishing with autofinish. Genome Res. 2001, 11 (4): 614-625. 10.1101/gr.171401.

Article
PubMed Central
CAS
PubMed
Google Scholar