SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

BMC Bioinformatics

Marten Boetzer¹  Walter Pirovano¹ 

[1] BaseClear B.V., Genome analysis and technology department, Einsteinweg 5, Leiden 2333 CC, The Netherlands

关键词: Genome finishing;    Pacific biosciences;    Single molecule sequencing;    Scaffolding;    De novo assembly;   

Others  :  818389
DOI  :  10.1186/1471-2105-15-211

 received in 2014-04-28, accepted in 2014-06-04,  发布年份 2014

【 摘 要 】

Background

The recent introduction of the Pacific Biosciences RS single molecule sequencing technology has opened new doors to scaffolding genome assemblies in a cost-effective manner. The long read sequence information is promised to enhance the quality of incomplete and inaccurate draft assemblies constructed from Next Generation Sequencing (NGS) data.

Results

Here we propose a novel hybrid assembly methodology that aims to scaffold pre-assembled contigs in an iterative manner using PacBio RS long read information as a backbone. On a test set comprising six bacterial draft genomes, assembled using either a single Illumina MiSeq or Roche 454 library, we show that even a 50× coverage of uncorrected PacBio RS long reads is sufficient to drastically reduce the number of contigs. Comparisons to the AHA scaffolder indicate our strategy is better capable of producing (nearly) complete bacterial genomes.

Conclusions

The current work describes our SSPACE-LongRead software which is designed to upgrade incomplete draft genomes using single molecule sequences. We conclude that the recent advances of the PacBio sequencing technology and chemistry, in combination with the limited computational resources required to run our program, allow to scaffold genomes in a fast and reliable manner.

【 授权许可】

   
2014 Boetzer and Pirovano; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

【 参考文献 】

• [1]Zerbino DR, Birney E: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18:821-829.
• [2]Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, Li H, Jian M, Li J, Zhang Z, Nielsen R, Li D, Gu W, Yang Z, Xuan Z, Ryder OA, Leung FC, Zhou Y, Cao J, Sun X, Fu Y, et al.: The sequence and de novo assembly of the giant panda genome. Nature 2010, 463:311-317.
• [3]Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I: ABySS: a parallel assembler for short read sequence data. Genome Res 2009, 19:1117-1123.
• [4]Dayarian A, Michael TP, Sengupta AM: SOPRA: Scaffolding algorithm for paired reads via statistical optimization. BMC Bioinformatics 2010, 11:345. BioMed Central Full Text
• [5]Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W: Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 2011, 27:578-579.
• [6]Salmela L, Mäkinen V, Välimäki N, Ylinen J, Ukkonen E: Fast scaffolding with small independent mixed integer programs. Bioinformatics 2011, 27:3259-3265.
• [7]Jiao X, Zheng X, Ma L, Kutty G, Gogineni E, Sun Q, Sherman BT, Hu X, Jones K, Raley C, Tran B, Munroe DJ, Stephens R, Liang D, Imamichi T, Kovacs JA, Lempicki RA, Huang DW: A benchmark study on error assessment and quality control of CCS reads derived from the PacBio RS. J Data Mining Genomics Proteomics 2013, 4:16008.
• [8]Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J: Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013, 10:563-569.
• [9]Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Adam MP: Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 2012, 30:693-700.
• [10]Au KF, Underwood JG, Lee L, Wong WH: Improving PacBio long read accuracy by short read alignment. PLoS One 2012, 7:e46679.
• [11]Goldberg SM, Johnson J, Busam D, Feldblyum T, Ferriera S, Friedman R, Halpern A, Khouri H, Kravitz SA, Lauro FM, Li K, Rogers YH, Strausberg R, Sutton G, Tallon L, Thomas T, Venter E, Frazier M, Venter JC: A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad Sci U S A 2006, 103:11240-11245.
• [12]Chevreux B, Wetter T, Suhai S: Genome sequence assembly using trace signals and a2ditional sequence information computer science and biology. Proc Ger Conf Bioinform 1999, 99:45-56.
• [13]Ribeiro FJ, Przybylski D, Yin S, Sharpe T, Gnerre S, Abouelleil A, Berlin AM, Montmayeur A, Shea TP, Walker BJ, Young SK, Russ C, Nusbaum C, MacCallum I, Jaffe DB: Finished bacterial genomes from shotgun sequence data. Genome Res 2012, 22:2270-2277.
• [14]Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, Scheutz F, Paxinos EE, Sebra R, Chin CS, Iliopoulos D, Klammer A, Peluso P, Lee L, Kislyuk AO, Bullard J, Kasarskis A, Wang S, Eid J, Rank D, Redman JC, Steyert SR, Frimodt-Møller J, Struve C, Petersen AM, Krogfelt KA, Nataro JP, Schadt EE, Waldor MK: Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 2011, 365:709-717.
• [15]Deshpande V, Fung EDK, Pham S, Bafna V: Cerulean: a hybrid assembly using high thoughput short and long reads. Algorithms Bioinform: Lect Notes Com Science 2013, 8126:349-363.
• [16]Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA: GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res 2012, 22:557-567.
• [17]English AC, Richards S, Han Y, Wang M, Vee V, Qu J, Qin X, Muzny DM, Reid JG, Worley KC, Gibbs RA: Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One 2012, 7(11):e47768.
• [18]Boisvert S, Laviolette F, Corbeil J: Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J Comput Biol 2010, 17:1519-1533.
• [19]Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM, McVey SD, Radune D, Bergman NH, Phillippy AM: Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biol 2013, 14:R101. BioMed Central Full Text
• [20]Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
• [21]Gurevich A1, Saveliev V, Vyahhi N, Tesler G: QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013, 29:1072-1075.
• [22]Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA: SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012, 19:455-477.
• [23]Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA: The MaSuRCA genome assembler. Bioinformatics 2013, 29:2669-2677.
• [24]Pacific Biosciences/Bioinformatics-training: circularizing and trimming https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Circularizing-and-trimming webcite
• [25]Chaisson MJ, Tesler G: Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics 2012, 13:238. BioMed Central Full Text