Mapping of Sequence Reads to the Reference Genomes    ◾    87

3. Smith TF, Waterman MS: Identification of common molecular subsequences. J Mol Biol 1981,

147(1):195–197.

4. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol

Biol 1990, 215(3):403–410.

5. Fredkin E: Trie memory. Commun ACM 1960, 3:490–499.

6. Ukkonen E: On-line construction of suffix trees. Algorithmica 1995, 14(3):249–260.

7. Shrestha AMS, Frith MC, Horton P: A bioinformatician’s guide to the forefront of suffix array

construction algorithms. Brief Bioinfor 2014, 15(2):138–154.

8. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras

TR: STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013, 29(1):15–21.

9. Li H, Durbin R: Fast and accurate short read alignment with Burrows–Wheeler transform.

Bioinformatics 2009, 25(14):1754–1760.

10. 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.

11. Fernandez E, Najjar W, Lonardi S: String Matching in Hardware Using the FM-Index. In:

2011 IEEE 19th Annual International Symposium on Field-Programmable Custom Computing

Machines: 1–3 May 2011 2011. 218–225.

12. Sankoff D, Kruskal J, Nerbonne J: Time Warps, String Edits, and Macromolecules: The Theory

and Practice of Sequence Comparison: Cambridge University Press; 2000.

13. Levin LA: Problems of Information Transmission. In: 1973.

14. Mu JC, Jiang H, Kiani A, Mohiyuddin M, Bani Asadi N, Wong WH: Fast and accurate read

alignment for resequencing. Bioinformatics 2012, 28(18):2366–2373.

15. Li R, Li Y, Kristiansen K, Wang J: SOAP: short oligonucleotide alignment program.

Bioinformatics 2008, 24(5):713–714.

16. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R:

The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25(16):2078–2079.

17. Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nature Methods 2012,

9(4):357–359.

18. Vasimuddin M, Misra S, Li H, Aluru S: Efficient Architecture-Aware Acceleration of BWA-

MEM for Multicore Systems. In: 2019 IEEE International Parallel and Distributed Processing

Symposium (IPDPS): 20–24 May 2019 2019. 314–324.

19. Otto TD, Dillon GP, Degrave WS, Berriman M: RATT: Rapid Annotation Transfer Tool.

Nucleic Acids Res 2011, 39(9):e57.