RandAL: A randomized approach to aligning DNA sequences to reference genomes

BMC Genomics

Volumn 15, Issue , 2014, Pages

  Vo, Nam S ^a   Tran, Quang ^b   Niraula, Nobal ^a   Phan, Vinhthuy ^a  

^a University of Memphis   (United States)

^b University of Memphis   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONTROLLED CLINICAL TRIAL; CONTROLLED STUDY; DNA SEQUENCE; GENOME; HUMAN; RANDOMIZED CONTROLLED TRIAL; SOFTWARE; VELOCITY; ALGORITHM; BIOLOGY; COMPUTER PROGRAM; HIGH THROUGHPUT SEQUENCING; PROCEDURES; SEQUENCE ALIGNMENT;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84921681944     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-S5-S2     Document Type: Article

References (15)

1. Langmead B, Trapnell C, Pop M, Salzberg SL, et al: Ultrafast and memoryefficient alignment of short dna sequences to the human genome. Genome Biol 2009, 10(3):25.
2. Li H, Durbin R: Fast and accurate short read alignment with burrowswheeler transform. Bioinformatics 2009, 25(14):1754-1760.
3. Langmead B, Salzberg SL: Fast gapped-read alignment with bowtie 2. Nature Methods 2012, 9(4):357-359.
4. Li H, Durbin R: Fast and accurate long-read alignment with burrowswheeler transform. Bioinformatics 2010, 26(5):589-595.
5. Li H, Ruan J, Durbin R: Mapping short dna sequencing reads and calling variants using mapping quality scores. Genome research 2008, 18(11):1851-1858.
6. Li R, Li Y, Kristiansen K, Wang J: Soap: short oligonucleotide alignment program. Bioinformatics 2008, 24(5):713-714.
7. Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M: Shrimp: accurate mapping of short color-space reads. PLoS computational biology 2009, 5(5):1000386.
8. Homer N, Merriman B, Nelson SF: Bfast: an alignment tool for large scale genome resequencing. PLoS One 2009, 4(11):7767.
9. Rizk G, Lavenier D: Gassst: global alignment short sequence search tool. Bioinformatics 2010, 26(20):2534-2540.
10. Ahmadi A, Behm A, Honnalli N, Li C, Weng L, Xie X: Hobbes: optimized gram-based methods for efficient read alignment. Nucleic Acids Research 2012, 40(6):41-41.
11. Weese D, Emde AK, Rausch T, Doring A, Reinert K: Razers-fast read mapping with sensitivity control. Genome Research 2009, 19(9):1646-1654.
12. Liu Y, Schmidt B: Long read alignment based on maximal exact match seeds. Bioinformatics 2012, 28(18):318-324.
13. Ferragina P, Manzini G: Indexing compressed text. J ACM 2005, 52(4):552-581.
14. Schatz M, Delcher A, Salzberg S: Assembly of large genomes using second-generation sequencing. Genome Research 2010, 20(9):1165-1173.
15. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Subgroup GPDP: The sequence alignment/map format and samtools. Bioinformatics 2009, 25(16):2078-2079.