Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler

BMC Genomics

Volumn 17, Issue 1, 2016, Pages

  Shepard, Samuel S ^a   Meno, Sarah ^a   Bahl, Justin ^b   Wilson, Malania M ^a,c   Barnes, John ^a   Neuhaus, Elizabeth ^a  

^a CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^b UNIVERSITY OF TEXAS SCHOOL OF PUBLIC HEALTH   (United States)

^c BATTELLE MEMORIAL INSTITUTE   (United States)

Author keywords

Deep sequencing; Ebola; High throughput; Influenza; NGS; Public health; Surveillance

Indexed keywords

ARTICLE; CONTROLLED STUDY; DEEP SEQUENCING; EBOLAVIRUS; GENE SEQUENCE; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; INFLUENZA VIRUS; NEXT GENERATION SEQUENCING; NONHUMAN; SOFTWARE; VIRUS ASSEMBLY; VIRUS GENOME; ALGORITHM; BIOLOGY; DNA SEQUENCE; GENETICS; HUMAN; PROCEDURES; SEQUENCE ANALYSIS; VIRUS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENOME, VIRAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA; SOFTWARE; VIRUSES;

EID: 84984972960     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-016-3030-6     Document Type: Article

References (43)

1. Reed C, Chaves SS, Daily Kirley P, Emerson R, Aragon D, Hancock EB, Butler L, Baumbach J, Hollick G, Bennett NM, et al. Estimating influenza disease burden from population-based surveillance data in the United States. PLoS One. 2015;10(3):e0118369.
2. FluNet: total influenza A and B specimens detected. http://www.who.int/influenza/gisrs_laboratory/flunet. Accessed 7 Nov 2015.
3. Westgeest KB, Russell CA, Lin X, Spronken MI, Bestebroer TM, Bahl J, van Beek R, Skepner E, Halpin RA, de Jong JC, et al. Genomewide analysis of reassortment and evolution of human influenza A(H3N2) viruses circulating between 1968 and 2011. J Virol. 2014;88(5):2844-57.
4. Gatherer D. The 2009 H1N1 influenza outbreak in its historical context. J Clin Virol. 2009;45(3):174-8.
5. Watson SJ, Welkers MR, Depledge DP, Coulter E, Breuer JM, de Jong MD, Kellam P. Viral population analysis and minority-variant detection using short read next-generation sequencing. Philos Trans R Soc Lond B Biol Sci. 2013;368(1614):20120205.
6. Wilm A, Aw PP, Bertrand D, Yeo GH, Ong SH, Wong CH, Khor CC, Petric R, Hibberd ML, Nagarajan N. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 2012;40(22):11189-201.
7. Wright CF, Morelli MJ, Thebaud G, Knowles NJ, Herzyk P, Paton DJ, Haydon DT, King DP. Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing. J Virol. 2011;85(5):2266-75.
8. Giallonardo FD, Topfer A, Rey M, Prabhakaran S, Duport Y, Leemann C, Schmutz S, Campbell NK, Joos B, Lecca MR, et al. Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations. Nucleic Acids Res. 2014;42(14):e115.
9. Yang X, Charlebois P, Gnerre S, Coole MG, Lennon NJ, Levin JZ, Qu J, Ryan EM, Zody MC, Henn MR. De novo assembly of highly diverse viral populations. BMC Genomics. 2012;13:475.
10. Whitmer SLM, Albariño C, Shepard SS, Dudas G, Sheth M, Brown SC, Cannon D, Erickson BR, Gibbons A, Schuh A et al. Preliminary Evaluation of the Effect of Investigational Ebola Virus Disease Treatments on Viral Genome Sequences. J Infect Dis. 2016. Ebolavirus Supplemental Issue.
11. Shepard SS, Davis CT, Bahl J, Rivailler P, York IA, Donis RO. LABEL: fast and accurate lineage assignment with assessment of H5N1 and H9N2 influenza A hemagglutinins. PLoS One. 2014;9(1):e86921.
12. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792-7.
13. Hunt M, Gall A, Ong SH, Brener J, Ferns B, Goulder P, Nastouli E, Keane JA, Kellam P, Otto TD. IVA: accurate de novo assembly of RNA virus genomes. Bioinformatics. 2015;31(14):2374-6.
14. Bewick V, Cheek L, Ball J. Statistics review 13: receiver operating characteristic curves. Crit Care. 2004;8(6):508-12.
15. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics. 2012;13(1):341.
16. Robasky K, Lewis NE, Church GM. The role of replicates for error mitigation in next-generation sequencing. Nat Rev Genet. 2014;15(1):56-62.
17. Base Quality Score Recalibration. [ https://www.broadinstitute.org/gatk/guide/article?id=44 ]. Accessed 30 Nov 2015.
18. Hwang S, Kim E, Lee I, Marcotte EM. Systematic comparison of variant calling pipelines using gold standard personal exome variants. Sci Rep. 2015;5:17875.
19. Browning SR, Browning BL. Haplotype phasing: existing methods and new developments. Nat Rev Genet. 2011;12(10):703-14.
20. Pecina P. A machine learning approach to multiword expression extraction. In: Proceedings of the LREC Workshop Towards a Shared Task for Multiword Expressions (MWE 2008): 2008. 2008. p. 54-61.
21. Chaudhari DL, Damani OP, Laxman S. Lexical co-occurrence, statistical significance, and word association. In: Proceedings of the Conference on Empirical Methods in Natural Language Processing: 2011. Association for Computational Linguistics; 2011. p. 1058-68
22. Zhou B, Wentworth DE. Influenza A virus molecular virology techniques. Methods Mol Biol. 2012;865:175-92.
23. Swofford DL. PAUP*: phylogenetic analysis using parsimony, version 4.0a146. 2011.
24. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30(14):3059-66.
25. Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ. Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009;25(9):1189-91.
26. Karplus K, Barrett C, Hughey R. Hidden Markov models for detecting remote protein homologies. Bioinformatics. 1998;14(10):846-56.
27. Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5(3):e9490.
28. Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res. 2002;12(4):656-64.
29. Siragusa E, Weese D, Reinert K. Fast and accurate read mapping with approximate seeds and multiple backtracking. Nucleic Acids Res. 2013;41(7):e78.
30. Siragusa E. Approximate string matching for high-throughput sequencing. Free University of Berlin; 2015. http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000099827.
31. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357-9.
32. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25.
33. Lee WP, Stromberg MP, Ward A, Stewart C, Garrison EP, Marth GT. MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping. PLoS One. 2014;9(3):e90581.
34. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer. Nat Biotechnol. 2011;29(1):24-6.
35. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078-9.
36. Zhao M, Lee W-P, Garrison EP, Marth GT. SSW library: an SIMD Smith-Waterman C/C++ library for use in genomic applications. PLoS One. 2013;8(12):e82138.
37. Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol. 1981;147(1):195-7.
38. Edgar RC, Flyvbjerg H. Error filtering, pair assembly and error correction for next-generation sequencing reads. Bioinformatics. 2015;31(21):3476-82.
39. Masella AP, Bartram AK, Truszkowski JM, Brown DG, Neufeld JD. PANDAseq: paired-end assembler for illumina sequences. BMC Bioinformatics. 2012;13:31.
40. Yang X, Chockalingam SP, Aluru S. A survey of error-correction methods for next-generation sequencing. Brief Bioinform. 2013;14(1):56-66.
41. Cai TT. One-sided confidence intervals in discrete distributions. J Statistical Planning and Inference. 2005;131(1):63-88.
42. Karlin S, Burge C. Dinucleotide relative abundance extremes: a genomic signature. Trends Genet. 1995;11(7):283-90.
43. Tange O. GNU Parallel - The Command-Line Power Tool. login: the USENIX Magazine. 2011. 36(1):42-47.