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Comparing de novo assemblers for 454 transcriptome data
Open accessAbstract
BACKGROUND: Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base) reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC) to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis. RESULTS: Although no single assembler performed best on all our criteria, Newbler 2.5 gave longer contigs, better alignments to some reference sequences, and was fast and easy to use. SeqMan assemblies performed best on the criterion of recapitulating known transcripts, and had more novel sequence than the other assemblers, but generated an excess of small, redundant contigs. The remaining assemblers all performed almost as well, with the exception of Newbler 2.3 (the version currently used by most assembly projects), which generated assemblies that had significantly lower total length. As different assemblers use different underlying algorithms to generate contigs, we also explored merging of assemblies and found that the merged datasets not only aligned better to reference sequences than individual assemblies, but were also more consistent in the number and size of contigs. CONCLUSIONS: Transcriptome assemblies are smaller than genome assemblies and thus should be more computationally tractable, but are often harder because individual contigs can have highly variable read coverage. Comparing single assemblers, Newbler 2.5 performed best on our trial data set, but other assemblers were closely comparable. Combining differently optimal assemblies from different programs however gave a more credible final product, and this strategy is recommended.
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“However, new assembly strategies such as merging the contigs of multiple assemblies [20], [21] and trimming of low-quality bases at the end of reads [22] can give better assembly results [9].”
From Digital Gene Expression Analysis Based on Integrated De Novo Transcriptome Assembly of Sweet Potato [Ipomoea batatas (L.) Lam.] (2012) · cites this paper as [21]
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Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Velvet: Algorithms for de novo short read assembly using de Bruijn graphsPreprint
Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,587
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
Genome sequencing in microfabricated high-density picolitre reactors
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693
CAP3: A DNA Sequence Assembly Program
Huang, X., & Madan, A. (1999) · Genome Research · doi:10.1101/gr.9.9.868 · Cited by 5,261
The COG database: an updated version includes eukaryotes
Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S., Nikolskaya, A. N., et al. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-41 · Cited by 4,470
An efficient algorithm for large-scale detection of protein families
Enright, A. J. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.7.1575 · Cited by 3,582
Pertea, G. M., Huang, X., Liang, F., Antonescu, V., Sultana, R., Karamycheva, S. A., Lee, Y., White, J., Cheung, F., Parvizi, B., et al. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg034 · Cited by 1,904
Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
Chevreux, B., Wetter, T. C., & Suhai, S. (1999) · Cited by 1,047
SSAHA: A Fast Search Method for Large DNA Databases
Ning, Z., Cox, A. J., & Mullikin, J. C. (2001) · Genome Research · doi:10.1101/gr.194201 · Cited by 965
Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
VERA, J. C., WHEAT, C. W., FESCEMYER, H. W., FRILANDER, M. J., CRAWFORD, D. L., HANSKI, I., & MARDEN, J. H. (2008) · Molecular Ecology · doi:10.1111/j.1365-294x.2008.03666.x · Cited by 714 · cited 1×
“…, Heliconius erato , and Melitaea cinxia [11]; TGICL Pythium ultimum [31]; Zoarces viviparous [32]; Medicago truncatula [33] SeqMan Melitaea cinxia [34]; Cochliomyia hominivorax [35]; Pinus contorta [36] stackPACK Arabidopsis thaliana [1] Table 2 Features of assembly programmes compared in this…”
BackgroundTablet-next generation sequence assembly visualization.
Milne, I., Bayer, M., Cardle, L., Shaw, P., Stephen, G., Wright, F., & Marshall, D. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp666 · Cited by 666
Draft Genome of the Filarial Nematode Parasite Brugia malayi
Ghedin, E., Wang, S., Spiro, D., Caler, E. V., Zhao, Q., Crabtree, J., Allen, J., Delcher, A. L., Guiliano, D. B., Miranda‐Saavedra, D., et al. (2007) · Science · doi:10.1126/science.1145406 · Cited by 622
Self-citationHigh-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome
Novaes, E., Drost, D. R., Farmerie, W. G., Pappas, G. J., Grattapaglia, D., Sederoff, R. R., & Kirst, M. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-312 · Cited by 493
Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx
Meyer, E., Aglyamova, G. V., Wang, S., Buchanan-Carter, J., Abrego, D., Colbourne, J. K., Willis, B. L., & Matz, M. V. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-219 · Cited by 479
Parchman, T. L., Geist, K. S., Grahnen, J. A., Benkman, C. W., & Buerkle, C. A. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-180 · Cited by 446
De novo transcriptome assembly with ABySS
Birol, İ., Jackman, S. D., Nielsen, C. B., Qian, J. Q., Varhol, R., Stazyk, G., Morin, R. D., Zhao, Y., Hirst, M., Schein, J. E., et al. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp367 · Cited by 403
Gene discovery and annotation using LCM-454 transcriptome sequencingPreprint
Emrich, S., Barbazuk, W. B., Li, L., & Schnable, P. S. (2006) · Genome Research · doi:10.1101/gr.5145806 · Cited by 381
Sampling the Arabidopsis Transcriptome with Massively Parallel Pyrosequencing
Weber, A. P. M., Weber, K. L., Carr, K. M., Wilkerson, C. G., & Ohlrogge, J. B. (2007) · PLANT PHYSIOLOGY · doi:10.1104/pp.107.096677 · Cited by 369
Microarray and cDNA sequence analysis of transcription during nerve-dependent limb regeneration
Monaghan, J. R., EPP, L. G., Putta, S., Page, R. B., Walker, J. A., Beachy, C. K., Zhu, W. Z., Pao, G. M., Verma, I. M., Hunter, T. R., et al. (2009) · BMC Biology · doi:10.1186/1741-7007-7-1 · Cited by 309
Sun, C., Li, Y., Wu, Q., Luo, H., Sun, Y., Song, J., Lui, E. M., & Chen, S. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-262 · Cited by 286
Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology
Cheung, F., Haas, B. J., Goldberg, S. M. D., May, G. D., Xiao, Y., & Town, C. D. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-272 · Cited by 247
Barakat, A., DiLoreto, D. S., Zhang, Y., Smith, C., Baier, K., Powell, W. A., Wheeler, N., Sederoff, R., & Carlson, J. E. (2009) · BMC Plant Biology · doi:10.1186/1471-2229-9-51 · Cited by 243
Zeng, S., Xiao, G., Guo, J., Fei, Z., Xu, Y., Roe, B. A., & Wāng, Y. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-94 · Cited by 231
A transcriptional sketch of a primary human breast cancer by 454 deep sequencing
Guffanti, A., Iacono, M., Pelucchi, P., Kim, N., Soldà, G., Croft, L., Taft, R. J., Rizzi, E., Askarian-Amiri, M., Bonnal, R. J. P., et al. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-163 · Cited by 231
Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing
Wang, W., Wang, Y., Zhang, Q., Qi, Y., & Guo, D. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-465 · Cited by 224
Comparison of next generation sequencing technologies for transcriptome characterization
Wall, P. K., Leebens‐Mack, J., Chanderbali, A. S., Barakat, A., Wolcott, E., Liang, H., Landherr, L. L., Tomsho, L. P., Hu, Y., Carlson, J. E., et al. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-347 · Cited by 213
Miller, R. T., Christoffels, A. G., Gopalakrishnan, C., Burke, J. P., Ptitsyn, A. A., Broveak, T. R., & Hide, W. A. (1999) · Genome Research · doi:10.1101/gr.9.11.1143 · Cited by 201
Clark, M. S., Thorne, M. A. S., Vieira, F. A., Cardoso, J. C. R., Power, D. M., & Peck, L. S. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-362 · Cited by 193
Pauchet, Y., Wilkinson, P. A., Vogel, H., Nelson, D. R., Reynolds, S., Heckel, D., & ffrench-Constant, R. (2010) · Insect molecular biology (Print) · doi:10.1111/j.1365-2583.2009.00936.x · Cited by 160
Zhang, F., Guo, H., Zheng, H., Zhou, T., Zhou, Y., Wang, S., Fang, R., Qian, W., & Chen, X. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-303 · Cited by 141
Swindell, S. R., & Plasterer, T. N. (1997) · Humana Press eBooks · doi:10.1385/0-89603-358-9:75 · Cited by 141
Hahn, D., Ragland, G. J., Shoemaker, D., & Denlinger, D. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-234 · Cited by 132
Of Mice, Cattle, and Humans: The Immunology and Treatment of River Blindness
Allen, J. E., Adjei, O., Bain, O., Hoerauf, A. M., Hoffmann, W. H., Makepeace, B. L., Schulz-Key, H., Tanya, V. N., Trees, A. J., Wanji, S., et al. (2008) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0000217 · Cited by 121
Transcript Profiling by 3′-Untranslated Region Sequencing Resolves Expression of Gene Families
Eveland, A. L., McCarty, D. R., & Koch, K. E. (2007) · PLANT PHYSIOLOGY · doi:10.1104/pp.107.108597 · Cited by 108
Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches
Cheung, F., Win, J., Lang, J. M., Hamilton, J. P., Vuong, H., Leach, J. E., Kamoun, S., Lévesque, C. A., Tisserat, N. A., & Buell, C. R. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-542 · Cited by 101
Timme, R. E. E., & Delwiche, C. (2010) · BMC Plant Biology · doi:10.1186/1471-2229-10-96 · Cited by 98
Schwarz, D., Robertson, H. M., Feder, J. L., Varala, K., Hudson, M. E., Ragland, G. J., Hahn, D. A., & Berlocher, S. H. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-633 · Cited by 95
Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing
Vega‐Arreguín, J., Ibarra‐Laclette, E., Jiménez-Moraila, B., Martínez, O., Vielle‐Calzada, J., Herrera‐Estrella, L., & Herrera‐Estrella, A. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-299 · Cited by 93
Pauchet, Y., Wilkinson, P., van Munster, M., Augustin, S., Pauron, D., & ffrench‐Constant, R. H. (2009) · Insect Biochemistry and Molecular Biology · doi:10.1016/j.ibmb.2009.04.001 · Cited by 92
Roeding, F., Borner, J., Kube, M., Klages, S., Reinhardt, R., & Burmester, T. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.08.014 · Cited by 91
Kristiansson, E., Asker, N., Förlin, L., & Larsson, D. G. J. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-345 · Cited by 90
Sequence Data Analysis Guidebook
(1997) · Humana Press eBooks · doi:10.1385/0896033589 · Cited by 89
Bellin, D., Ferrarini, A., Chimento, A., Kaiser, O., Levenkova, N., Bouffard, P., & Delledonne, M. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-555 · Cited by 89
Ferguson, L., Lee, S. F., Chamberlain, N. L., Nadeau, N. J., Joron, M., Baxter, S. W., Wilkinson, P. A., Papanicolaou, A., Kumar, S., KEE, T., et al. (2010) · Molecular Ecology · doi:10.1111/j.1365-294x.2009.04475.x · Cited by 82
Self-citationZagrobelny, M., Scheibye-Alsing, K., Jensen, N. B., Møller, B. L., Gorodkin, J., & Bak, S. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-574 · Cited by 80
Next generation transcriptomes for next generation genomes using est2assembly
Papanicolaou, A., Stierli, R., ffrench-Constant, R., & Heckel, D. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-447 · Cited by 70
Rapid transcriptome and proteome profiling of a non‐model marine invertebrate, Bugula neritina
Wang, H., Zhang, H., Wong, Y. H., Voolstra, C. R., Ravasi, T., Bajić, V. B., & Qian, P. (2010) · PROTEOMICS · doi:10.1002/pmic.201000056 · Cited by 63
Cantacessi, C., Campbell, B. E., Young, N. D., Jex, A. R., Hall, R. S., Presidente, P. J. A., Zawadzki, J. L., Zhong, W., Boanerges Aleman-meza, A., Loukas, A. C., et al. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-266 · Cited by 56
Schmid, J., Müller-Hagen, D., Bekel, T., Funk, L., Ståhl, U., Sieber, V., & Meyer, V. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-329 · Cited by 52
PAVE: Program for assembling and viewing ESTs
Soderlund, C. A., Johnson, E., Bomhoff, M., & Descour, A. S. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-400 · Cited by 38
Assembling genomes using short-read sequencing technology
Jackman, S. D., & Birol, İ. (2010) · Genome biology · doi:10.1186/gb-2010-11-1-202 · Cited by 30
Palmieri, N., & Schlötterer, C. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006323 · Cited by 29
A Database of Expressed Genes FromCochliomyia hominivorax(Diptera: Calliphoridae)
Guerrero, F. D., Dowd, S. E., Djikeng, A., Wiley, G. B., Macmil, S. L., Saldivar, L., Najar, F. Z., & Roe, B. A. (2009) · Journal of Medical Entomology · doi:10.1603/033.046.0518 · Cited by 22
SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses
Barker, M. S., Dlugosch, K. M., Reddy, A. C. C., Amyotte, S. N., & Rieseberg, L. H. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp011 · Cited by 19
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Metadata
- Authors
- Kumar, S., & Blaxter, M. L.
- Affiliations
- University of Edinburgh (GB)
- Corresponding author
- Blaxter, Mark L
- Venue
- BMC Genomics
- Published
- 2010-10-16
- Volume
- 11
- Issue
- 1
- Pages
- 571-571
- ISSN
- 1471-2164 (ISSN-L)
- PMC
- PMC3091720
- OpenAlex
- W2100703845
- Cited by
- 255
- References
- 55
- Citations by year
- 2026: 1 · 2025: 3 · 2022: 2 · 2021: 3 · 2020: 11 · 2019: 4 · 2018: 7 · 2017: 12 · 2016: 22 · 2015: 22 · 2014: 44 · 2013: 38 · 2012: 52
- FWCI
- 16.14
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Genomics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
- Funders
- Directorate for Biological Sciences
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- transcriptome assembly, de novo assembly, 454 pyrosequencing, assembler comparison, CAP3, Mira, CLC, parasitic nematodes, Litomosoides sigmodontis, non-model organisms
- MeSH terms
- Algorithms, Animals, Base Sequence, Female, Filarioidea, Gene Expression Regulation, Male, Reference Standards, Temperature, Reproducibility of Results, Sequence Alignment, Sequence Analysis, DNA, Expressed Sequence Tags, Contig Mapping, Gene Expression Profiling, Databases, Genetic
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