Evaluation of de novo transcriptome assemblies from RNA-Seq data

Genome Biology

Volumn 15, Issue 12, 2014, Pages

  Li, Bo ^a   Fillmore, Nathanael ^b   Bai, Yongsheng ^c   Collins, Mike ^d   Thomson, James A ^d,e,f   Stewart, Ron ^d   Dewey, Colin N ^b,f  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of Wisconsin Madison   (United States)

^c INDIANA STATE UNIVERSITY   (United States)

^d MORGRIDGE INSTITUTE FOR RESEARCH   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; TRANSCRIPTOME;

ACCURACY; ALGORITHM; ARTICLE; COMPUTER PROGRAM; GENE EXPRESSION; GENOME; INTERNET; PROTEIN ASSEMBLY; RNA SEQUENCE; SCORING SYSTEM; UPREGULATION; ANIMAL; BIOLOGY; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; PROCEDURES; SEQUENCE ANALYSIS;

AMBYSTOMA MEXICANUM;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84924629458     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-014-0553-5     Document Type: Article

References (53)

1. Martin J, Bruno VM, Fang Z, Meng X, Blow M, Zhang T, Sherlock G, Snyder M, Wang Z: Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. BMC Genomics2010, 11:663.
2. Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu A-L, Tam A, Zhao Y, Moore RA, Hirst M, Marra MA, Jones SJ, Hoodless PA, Birol I: De novo assembly and analysis of RNA-seq data. Nat Methods2010, 7:909-912.
3. Surget-Groba Y, Montoya-Burgos JI: Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res2010, 20:1432-1440.
4. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol2011, 29:644-652.
5. Chen C-C, Lin W-D, Chang Y-J, Chen C-L, Ho J-M: Enhancing de novo transcriptome assembly by incorporating multiple overlap sizes. ISRN Bioinformatics2012, 2012:816402.
6. Schulz MH, Zerbino DR, Vingron M, Birney E: Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics2012, 28:1086-1092.
7. Chu H-T, Hsiao WWL, Chen J-C, Yeh T-J, Tsai M-H, Lin H, Liu Y-W, Lee S-A, Chen C-C, Tsao TTH, Kao C-Y: EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection. Bioinformatics2013, 29:1004-1010.
8. Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, Huang W, He G, Gu S, Li S, Zhou X, Lam T-W, Li Y, Xu X, Wong GK, Wang J: SOAPdenovo-Trans de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics2014, 30:1660-1666.
9. Huang X, Madan A: CAP3: a DNA sequence assembly program. Genome Res1999, 9:868-877.
10. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WE, Wetter T, Suhai S: Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res2004, 14:1147-1159.
11. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, et al: Genome sequencing in microfabricated high-density picolitre reactors. Nature2005, 437:376-380.
12. Zheng Y, Zhao L, Gao J, Fei Z: iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinformatics2011, 12:453.
13. Kumar S, Blaxter ML: Comparing de novo assemblers for 454 transcriptome data. BMC Genomics2010, 11:571.
14. Feldmeyer B, Wheat CW, Krezdorn N, Rotter B, Pfenninger M: Short read Illumina data for the de novo assembly of a non-model snail species transcriptome ( Radix balthica, Basommatophora, Pulmonata ), and a comparison of assembler performance. BMC Genomics2011, 12:317.
15. Zhao Q-Y, Wang Y, Kong Y-M, Luo D, Li X, Hao P: Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics2011, 12:S2.
16. Mundry M, Bornberg-Bauer E, Sammeth M, Feulner PGD: Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach. PLoS One2012, 7:e31410.
17. Ren X, Liu T, Dong J, Sun L, Yang J, Zhu Y, Jin Q: Evaluating de Bruijn graph assemblers on 454 transcriptomic data. PLoS One2012, 7:e51188.
18. Clarke K, Yang Y, Marsh R, Xie L, Zhang KK: Comparative analysis of de novo transcriptome assembly. Sci China Life Sci2013, 56:156-162.
19. Lu B, Zeng Z, Shi T: Comparative study of de novo assembly and genome-guided assembly strategies for transcriptome reconstruction based on RNA-Seq. Sci China Life Sci2013, 56:143-155.
20. O'Neil ST, Emrich SJ: Assessing de novo transcriptome assembly metrics for consistency and utility. BMC Genomics2013, 14:465.
21. Miller JR, Koren S, Sutton G: Assembly algorithms for next-generation sequencing data. Genomics2010, 95:315-327.
22. 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 Res2012, 22:557-567.
23. Rahman A, Pachter L: CGAL: computing genome assembly likelihoods. Genome Biol2013, 14:R8.
24. Laserson J, Jojic V, Koller D: Genovo de novo assembly for metagenomes. J Comput Biol2011, 18:429-443.
25. Clark SC, Egan R, Frazier PI, Wang Z: ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies. Bioinformatics2013, 29:435-443.
26. O'Neil ST, Dzurisin JDK, Carmichael RD, Lobo NF, Emrich SJ, Hellmann JJ: Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon. BMC Genomics2010, 11:310.
27. Stewart R, Rascon CA, Tian S, Nie J, Barry C, Chu LF, Ardalani H, Wagner RJ, Probasco MD, Bolin JM, Leng N, Sengupta S, Volkmer M, Habermann B, Tanaka EM, Thomson JA, Dewey CN: Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema. PLoS Comput Biol2013, 9:e1002936.
28. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res1997, 25:3389-3402.
29. Tam W-L, Lim B: Genome-wide transcription factor localization and function in stem cells. In StemBook. Edited by Girard L. Cambridge, MA: Harvard Stem Cell Institute; 2008.
30. Zakany J, Duboule D: The role of jHox genes during vertebrate limb development. Curr Opin Genet Dev2007, 17:359-366.
31. Koshiba K, Kuroiwa A, Yamamoto H, Tamura K, Ide H: Expression of Msx genes in regenerating and developing limbs of axolotl. J Exp Zool1998, 282:703-714.
32. Clement-Jones M, Schiller S, Rao E, Blaschke RJ, Zuniga A, Zeller R, Robson SC, Binder G, Glass I, Strachan T, Lindsay S, Rappold GA: The short stature homeobox gene SHOX is involved in skeletal abnormalities in Turner syndrome. Hum Mol Genet2000, 9:695-702.
33. Phillippy AM, Schatz MC, Pop M: Genome assembly forensics: finding the elusive mis-assembly. Genome Biol2008, 9:R55.
34. Darling AE, Tritt A, Eisen JA, Facciotti MT: Mauve assembly metrics. Bioinformatics2011, 27:2756-2757.
35. Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HOK, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung W-K, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol I, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, et al: Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res2011, 21:2224-2241.
36. Lin Y, Li J, Shen H, Zhang L, Papasian CJ, Deng H-W: Comparative studies of de novo assembly tools for next-generation sequencing technologies. Bioinformatics2011, 27:2031-2037.
37. Narzisi G, Mishra B: Comparing de novo genome assembly: the long and short of it. PLoS One2011, 6:e19175.
38. Zhang W, Chen J, Yang Y, Tang Y, Shang J, Shen B: A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies. PLoS One2011, 6:e17915.
39. Vezzi F, Narzisi G, Mishra B: Feature-by-feature - evaluating de novo sequence assembly. PLoS One2012, 7:e31002.
40. Gurevich A, Saveliev V, Vyahhi N, Tesler G: QUAST: quality assessment tool for genome assemblies. Bioinformatics2013, 29:1072-1075.
41. Howison M, Zapata F, Dunn CW: Toward a statistically explicit understanding of de novo sequence assembly. Bioinformatics2013, 29:2959-2963.
42. Schwarz G: Estimating the dimension of a model. Ann Stat1978, 6:461-464.
43. Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN: RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics2010, 26:493-500.
44. Li B, Dewey CN: RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics2011, 12:323.
45. Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol2009, 10:R25.
46. Marco-Sola S, Sammeth M, Guigó R, Ribeca P: The GEM mapper: fast, accurate and versatile alignment by filtration. Nat Methods2012, 9:1185-1188.
47. Kent WJ: BLAT - the BLAST-like alignment tool. Genome Res2002, 12:656-664.
48. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GRS, Ruffier M, Schuster M, et al: Ensembl 2011. Nucleic Acids Res2011, 39:D800-D806.
49. Trapnell C, Williams B, Pertea G, Mortazavi A, Kwan G, van Baren M, Salzberg SL, Wold B, Pachter L: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol2010, 28:511-515.
50. Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG: PomBase: a comprehensive online resource for fission yeast. Nucleic Acids Res2012, 40:D695-D699.
51. Magrane M, UniProt Consortium: UniProt knowledgebase: a hub of integrated protein data. Database2011, 2011:bar009.
52. DETONATE website[ http://deweylab.biostat.wisc.edu/detonate ]
53. DETONATE source code[ https://github.com/deweylab/detonate ]