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ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
Iain MacCallum, Dariusz Przybylski, Sante Gnerre, Joshua Burton, Ilya Shlyakhter, Andreas Gnirke, Joel Malek, Kevin McKernan, Swati Ranade, Terrance P Shea, Louise Williams, Sarah Young, Chad Nusbaum, David B Jaffe
Genome Biol. 2009; 10(10): R103. Published online 2009 October 1. doi: 10.1186/gb-2009-10-10-r103
PMCID:
PMC2784318
Abstract Full Text PDF–195K Supplementary Material
 Is Cited by the Following 24 Articles in this Archive:
Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
Isheng J Tsai, Thomas D Otto, Matthew Berriman
Genome Biol. 2010; 11(4): R41. Published online 2010 April 13. doi: 10.1186/gb-2010-11-4-r41
PMCID:
PMC2884544
Abstract Full Text PDF–1.2M Supplementary Material
Read Length and Repeat Resolution: Exploring Prokaryote Genomes Using Next-Generation Sequencing Technologies
Matt J. Cahill, Claudio U. Köser, Nicholas E. Ross, John A. C. Archer
PLoS One. 2010; 5(7): e11518. Published online 2010 July 12. doi: 10.1371/journal.pone.0011518
PMCID:
PMC2902515
Abstract Full Text PDF–695K Supplementary Material
A computational genomics pipeline for prokaryotic sequencing projects
Andrey O. Kislyuk, Lee S. Katz, Sonia Agrawal, Matthew S. Hagen, Andrew B. Conley, Pushkala Jayaraman, Viswateja Nelakuditi, Jay C. Humphrey, Scott A. Sammons, Dhwani Govil, Raydel D. Mair, Kathleen M. Tatti, Maria L. Tondella, Brian H. Harcourt, Leonard W. Mayer, I. King Jordan
Bioinformatics. 2010 August 1; 26(15): 1819–1826. Published online 2010 June 2. doi: 10.1093/bioinformatics/btq284
PMCID:
PMC2905547
Abstract Full Text PDF–2.8M Supplementary Material
Integrating genome assemblies with MAIA
Jurgen Nijkamp, Wynand Winterbach, Marcel van den Broek, Jean-Marc Daran, Marcel Reinders, Dick de Ridder
Bioinformatics. 2010 September 15; 26(18): i433–i439. Published online 2010 September 4. doi: 10.1093/bioinformatics/btq366
PMCID:
PMC2935414
Abstract Full Text PDF–562K
De Novo Transcriptome Sequencing in Anopheles funestus Using Illumina RNA-Seq Technology
Jacob E. Crawford, Wamdaogo M. Guelbeogo, Antoine Sanou, Alphonse Traoré, Kenneth D. Vernick, N'Fale Sagnon, Brian P. Lazzaro
PLoS One. 2010; 5(12): e14202. Published online 2010 December 2. doi: 10.1371/journal.pone.0014202
PMCID:
PMC2996306
Abstract Full Text PDF–513K Supplementary Material
Studying bacterial transcriptomes using RNA-seq
Nicholas J Croucher, Nicholas R Thomson
Curr Opin Microbiol. 2010 October; 13(5): 619–624. doi: 10.1016/j.mib.2010.09.009
PMCID:
PMC3025319
Abstract Full Text
Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data
Miguel Pignatelli, Andrés Moya
PLoS One. 2011; 6(5): e19984. Published online 2011 May 23. doi: 10.1371/journal.pone.0019984
PMCID:
PMC3100316
Abstract Full Text PDF–442K Supplementary Material
Assembly Algorithms for Next-Generation Sequencing Data
Jason R. Miller, Sergey Koren, Granger Sutton
Genomics. Author manuscript; available in PMC 2011 June 1.
Published in final edited form as: Genomics. 2010 June; 95(6): 315–327. Published online 2010 March 6. doi: 10.1016/j.ygeno.2010.03.001
PMCID:
PMC2874646
Abstract Full Text PDF–367K
Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
Nynke L. van Berkum, Erez Lieberman-Aiden, Louise Williams, Maxim Imakaev, Andreas Gnirke, Leonid A. Mirny, Job Dekker, Eric S. Lander
J Vis Exp. 2010; (39): 1869. Published online 2010 May 6. doi: 10.3791/1869
PMCID:
PMC3149993
Abstract Full Text PDF–540K
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
Jarrod A. Chapman, Isaac Ho, Sirisha Sunkara, Shujun Luo, Gary P. Schroth, Daniel S. Rokhsar
PLoS One. 2011; 6(8): e23501. Published online 2011 August 18. doi: 10.1371/journal.pone.0023501
PMCID:
PMC3158087
Abstract Full Text PDF–336K Supplementary Material
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
Daniel Aird, Michael G Ross, Wei-Sheng Chen, Maxwell Danielsson, Timothy Fennell, Carsten Russ, David B Jaffe, Chad Nusbaum, Andreas Gnirke
Genome Biol. 2011; 12(2): R18. Published online 2011 February 21. doi: 10.1186/gb-2011-12-2-r18
PMCID:
PMC3188800
Abstract Full Text PDF–465K Supplementary Material
Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences
Song Gao, Wing-Kin Sung, Niranjan Nagarajan
J Comput Biol. 2011 November; 18(11): 1681–1691. doi: 10.1089/cmb.2011.0170
PMCID:
PMC3216105
Abstract Full Text PDF–1.7M
Metagenomic Insights into the Evolution, Function, and Complexity of the Planktonic Microbial Community of Lake Lanier, a Temperate Freshwater Ecosystem
Seungdae Oh, Alejandro Caro-Quintero, Despina Tsementzi, Natasha DeLeon-Rodriguez, Chengwei Luo, Rachel Poretsky, Konstantinos T. Konstantinidis
Appl Environ Microbiol. 2011 September; 77(17): 6000–6011. doi: 10.1128/AEM.00107-11
PMCID:
PMC3165412
Abstract Full Text PDF–2.2M Supplementary Material
AGORA: Assembly Guided by Optical Restriction Alignment
Henry C Lin, Steve Goldstein, Lee Mendelowitz, Shiguo Zhou, Joshua Wetzel, David C Schwartz, Mihai Pop
BMC Bioinformatics. 2012; 13: 189. Published online 2012 August 2. doi: 10.1186/1471-2105-13-189
PMCID:
PMC3431216
Abstract Full Text PDF–914K Supplementary Material
Telescoper: de novo assembly of highly repetitive regions
Ma'ayan Bresler, Sara Sheehan, Andrew H. Chan, Yun S. Song
Bioinformatics. 2012 September 15; 28(18): i311–i317. Published online 2012 September 3. doi: 10.1093/bioinformatics/bts399
PMCID:
PMC3436826
Abstract Full Text PDF–636K
Arapan-S: a fast and highly accurate whole-genome assembly software for viruses and small genomes
Mohammed Sahli, Tetsuo Shibuya
BMC Res Notes. 2012; 5: 243. Published online 2012 May 16. doi: 10.1186/1756-0500-5-243
PMCID:
PMC3441218
Abstract Full Text PDF–949K
Toward almost closed genomes with GapFiller
Marten Boetzer, Walter Pirovano
Genome Biol. 2012; 13(6): R56. Published online 2012 June 25. doi: 10.1186/gb-2012-13-6-r56
PMCID:
PMC3446322
Abstract Full Text PDF–413K
FLASH: fast length adjustment of short reads to improve genome assemblies
Tanja Magoč, Steven L. Salzberg
Bioinformatics. 2011 November 1; 27(21): 2957–2963. Published online 2011 September 7. doi: 10.1093/bioinformatics/btr507
PMCID:
PMC3198573
Abstract Full Text PDF–489K
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
Toshiaki Namiki, Tsuyoshi Hachiya, Hideaki Tanaka, Yasubumi Sakakibara
Nucleic Acids Res. 2012 November; 40(20): e155. Published online 2012 July 19. doi: 10.1093/nar/gks678
PMCID:
PMC3488206
Abstract Full Text PDF–2.4M Supplementary Material
Molecular Diagnosis of Infantile Mitochondrial Disease with Targeted Next-Generation Sequencing
Sarah E. Calvo, Alison G. Compton, Steven G. Hershman, Sze Chern Lim, Daniel S. Lieber, Elena J. Tucker, Adrienne Laskowski, Caterina Garone, Shangtao Liu, David B. Jaffe, John Christodoulou, Janice M. Fletcher, Damien L Bruno, Jack Goldblatt, Salvatore DiMauro, David R. Thorburn, Vamsi K. Mootha
Sci Transl Med. Author manuscript; available in PMC 2012 December 17.
Published in final edited form as: Sci Transl Med. 2012 January 25; 4(118): 118ra10. doi: 10.1126/scitranslmed.3003310
PMCID:
PMC3523805
Abstract Full Text PDF–1.7M Supplementary Material
State of the art de novo assembly of human genomes from massively parallel sequencing data
Yingrui Li, Yujie Hu, Lars Bolund, Jun Wang
Hum Genomics. 2010; 4(4): 271–277. Published online 2010 April 1. doi: 10.1186/1479-7364-4-4-271
PMCID:
PMC3525208
Abstract Full Text PDF–85K
Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly
Yen-Chun Chen, Tsunglin Liu, Chun-Hui Yu, Tzen-Yuh Chiang, Chi-Chuan Hwang
PLoS One. 2013; 8(4): e62856. Published online 2013 April 29. doi: 10.1371/journal.pone.0062856
PMCID:
PMC3639258
Abstract Full Text PDF–9.7M Supplementary Material
Fine De Novo Sequencing of a Fungal Genome Using only SOLiD Short Read Data: Verification on Aspergillus oryzae RIB40
Myco Umemura, Yoshinori Koyama, Itaru Takeda, Hiroko Hagiwara, Tsutomu Ikegami, Hideaki Koike, Masayuki Machida
PLoS One. 2013; 8(5): e63673. Published online 2013 May 7. doi: 10.1371/journal.pone.0063673
PMCID:
PMC3646829
Abstract Full Text PDF–1.2M Supplementary Material
Adaptin evolution in kinetoplastids and emergence of the variant surface glycoprotein coat in African trypanosomatids
Paul T. Manna, Steven Kelly, Mark C. Field
Mol Phylogenet Evol. 2013 April; 67(1): 123–128. doi: 10.1016/j.ympev.2013.01.002
PMCID:
PMC3650584
Abstract Full Text Supplementary Material