Comparison of mapping algorithms used in high-throughput sequencing: Application to Ion Torrent data

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Caboche, Ségolène ^a   Audebert, Christophe ^a,b   Lemoine, Yves ^a,c   Hot, David ^a,c  

^a INSTITUT PASTEUR DE LILLE   (France)

^b Genes Diffusion   (France)

^c UNIV LILLE   (France)

Author keywords

High throughput sequencing; Mapper comparison; Mapping algorithms; Read simulator

Indexed keywords

ACCURACY; ANALYTICAL ERROR; ARTICLE; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; DATA SYNTHESIS; GENE MAPPING; GENETIC ALGORITHM; GENETIC DATABASE; GENETIC VARIABILITY; GENOME ANALYSIS; HIGH THROUGHPUT SEQUENCING; INDEL MUTATION; INFORMATION RETRIEVAL; INFORMATION STORAGE; MATHEMATICAL COMPUTING; PROCESS DEVELOPMENT; SIMULATION;

ALGORITHMS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INTERNET; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SOFTWARE;

EID: 84897960349     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-264     Document Type: Article

References (30)

1. Soon WW, Hariharan M, Snyder MP. High-throughput sequencing for biology and medicine. Mol Syst Biol 2013, 9(640). [http://www.ncbi.nlm.nih.gov/pubmed/23340846].
2. Fonseca NA, Rung J, Brazma A, Marioni JC. Tools for mapping high-throughput sequencing data. Bioinformatics 2012, [http://bioinformatics.oxfordjournals.org/content/early/2012/10/11/bioinformatics.bts605.abstract].
3. Li H, Homer N. A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinformatics 2010, 11(5):473-483. 10.1093/bib/bbq015, 2943993, 20460430.
4. Bao S, Jiang R, Kwan W, Wang B, Ma X, Song YQ. Evaluation of next-generation sequencing software in mapping and assembly. J Hum Genet 2011, 56(6):406-414. 10.1038/jhg.2011.43, 21525877.
5. Ruffalo M, LaFramboise T, Koyutürk M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics 2011, [http://bioinformatics.oxfordjournals.org/content/27/20/2790].
6. Holtgrewe M, Emde AK, Weese D, Reinert K. A novel and well-defined benchmarking method for second generation read mapping. BMC Bioinformatics 2011, 12:210. [http://www.biomedcentral.com/1471-2105/12/210], 10.1186/1471-2105-12-210, 3128034, 21615913.
7. Schbath S, Martin V, Zytnicki M, Fayolle J, Loux V, Gibrat JF. Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. J Comput Biol 2012, 19(6):796-813. 10.1089/cmb.2012.0022, 3375638, 22506536.
8. Hatem A, Bozdag D, Toland AE, Catalyurek UV. Benchmarking short sequence mapping tools. BMC Bioinformatics 2013, 14:184. 10.1186/1471-2105-14-184, 3694458, 23758764.
9. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008, 36(16):e105. 10.1093/nar/gkn425, 2532726, 18660515.
10. Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, Frazer KA. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 2009, 10(3):R32. 10.1186/gb-2009-10-3-r32, 2691003, 19327155.
11. Meacham F, Boffelli D, Dhahbi J, Martin DI, Singer M, Pachter L. Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics 2011, 12:451. 10.1186/1471-2105-12-451, 3295828, 22099972.
12. Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 2012, 30(5):434-439. 10.1038/nbt.2198, 22522955.
13. Torok ME, Peacock SJ. Rapid whole-genome sequencing of bacterial pathogens in the clinical microbiology laboratory-pipe dream or reality?. J Antimicrob Chemother 2012, 67(10):2307-2308. 10.1093/jac/dks247, 22729921.
14. Sherry NL, Porter JL, Seemann T, Watkins A, Stinear TP, Howden BP. Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory. J Clin Microbiol 2013, 51(5):1396-1401. 10.1128/JCM.03332-12, 3647928, 23408689.
15. Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. eprint. 2012, (arXiv:1207.3907v2).
16. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9(4):357-359. 10.1038/nmeth.1923, 3322381, 22388286.
17. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
18. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010, 26(5):589-595. 10.1093/bioinformatics/btp698, 2828108, 20080505.
19. Wu TD, Nacu S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 2010, 26(7):873-881. [http://bioinformatics.oxfordjournals.org/content/26/7/873.abstract], 10.1093/bioinformatics/btq057, 2844994, 20147302.
20. Lee W, Stromberg M, Ward A, Stewart C, Garrison E, Marth G. MOSAIK: a hash-based algorithm for accurate next-generation sequencing read mapping. eprint arXiv:1309.1149 2013, [http://arxiv.org/abs/1309.1149].
21. Campagna D, Albiero A, Bilardi A, Caniato E, Forcato C, Manavski S, Vitulo N, Valle G. PASS: a program to align short sequences. Bioinformatics 2009, 25(7):967-968. [http://bioinformatics.oxfordjournals.org/content/25/7/967.abstract], 10.1093/bioinformatics/btp087, 19218350.
22. Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermuller J. Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol 2009, 5(9):e1000502. 10.1371/journal.pcbi.1000502, 2730575, 19750212.
23. David M, Dzamba M, Lister D, Ilie L, Brudno M. SHRiMP2: sensitive yet practical SHort Read Mapping. Bioinformatics 2011, 27(7):1011-1012. 10.1093/bioinformatics/btr046, 21278192.
24. Zaharia M, Bolosky WJ, Curtis K, Fox A, Patterson DA, Shenker S, Stoica I, Karp RM, Sittler T. Faster and more accurate sequence alignment with SNAP. CoRR 2011, abs/1111.5572.
25. Gontarz PM, Berger J, Wong CF. SRmapper: a fast and sensitive genome-hashing alignment tool. Bioinformatics 2012, [http://bioinformatics.oxfordjournals.org/content/early/2012/12/20/bioinformatics.bts712.abstract].
26. Ning Z, Cox AJ, Mullikin JC. SSAHA: a fast search method for large DNA databases. Genome Res 2001, 11(10):1725-1729. 10.1101/gr.194201, 311141, 11591649.
27. Homer N, Merriman B. TMAP: the Torrent Mapping Alignment Program. [https://github.com/iontorrent/TMAP].
28. Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, Macalalad AR, Berlin AM, Malboeuf CM, Ryan EM, Gnerre S, Zody MC, Erlich RL, Green LM, Berical A, Wang Y, Casali M, Streeck H, Bloom AK, Dudek T, Tully D, Newman R, Axten KL, Gladden AD, Battis L, Kemper M, Zeng Q, Shea TP, Gujja S, Zedlack C, Gasser O, et al. Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog 2012, 8(3):e1002529. 10.1371/journal.ppat.1002529, 3297584, 22412369.
29. Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M. Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012, 2012:251364. 3398667, 22829749.
30. 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, 13:341. 10.1186/1471-2164-13-341, 3431227, 22827831.