TriageTools: Tools for partitioning and prioritizing analysis of high-throughput sequencing data

Nucleic Acids Research

Volumn 41, Issue 7, 2013, Pages

  Fimereli, Danai ^a   Detours, Vincent ^a   Konopka, Tomasz ^a  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; GENE; GENE MAPPING; GENETIC DATABASE; HIGH THROUGHPUT SEQUENCING; HUMAN; INTERNET; PRIORITY JOURNAL; RNA SEQUENCE;

ALGORITHMS; GENES; GENES, NEOPLASM; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; RECEPTOR, NOTCH1; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84876516012     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt094     Document Type: Article

References (24)

1. The 1000 Genomes Project Consortium. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.
2. Thomas, T., Gilbert, J. and Meyer, F. (2012) Metagenomics- A guide from sampling to data analysis. Microb. Inform. Exp., 2, 3.
3. Curtis, C., Shah, S.P., Chin, S.F., Turashvili, G., Rueda, O.M., Dunning, M.J., Speed, D., Lynch, A.G., Samarajiwa, S., Yuan, Y. et al. (2012) The genomic and transcriptomic architecture of 2, 000 breast tumours reveals novel subgroups. Nature, 486, 346-352.
4. Sayers, E.W., Barrett, T., Benson, D.A., Bolton, E., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Federhen, S. et al. (2011) Database resources of the national center for biotechnology information. Nucleic Acids Res, 39, D38-D51.
5. Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
6. Wu, T.D. and Nacu, S. (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics, 26, 873-881.
7. Li, R., Yu, C., Li, Y., Lam, T.W., Yiu, S.M., Kristiansen, K. and Want, J. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 25, 1966-1967.
8. Zaharia, M., Bolosky, W.J., Curtis, K., Fox, A., Patterson, D., Shenker, S., Stoica, I., Karp, R.M. and Sittler, T. (2011) Faster and more accurate sequence alignment with SNAP. arXiv: 1111.5572.
9. Alkan, C., Kidd, J.M., Marques-Bonet, T., Aksay, G., Antonacci, F., Hormozdiari, F., Kitzman, J.O., Baker, C., Malig, M., Mutlu, O. et al. (2009) Personalized copy number and segmental duplication maps using next-generation sequencing. Nat. Genet., 41, 1061-1068.
10. Weese, D., Holtgrewe, M. and Reinert, K. (2012) RazerS 3: faster, fully sensitive read mapping. Bioinformatics, 28, 2592-2599.
11. Weese, D., Emde, A.K., Rausch, T., Doring, A. and Reinert, K. (2009) RazerS-fast read mapping with sensitivity control. Genome Res., 19, 1646-1656.
12. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., and 1000 Genome Project Data Processing Subgroup. (2009) The sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-2079.
13. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M. et al. (2010) Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res., 20, 1297-1303.
14. McPherson, A., Hormozdiari, F., Zayed, A., Giuliany, R., Ha, G., Sun, M.G.F., Griffith, M., Moussavi, A.H., Senz, J., Melnyk, N. et al. (2011) deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLOS Comput. Biol., 7, e1001138.
15. Kent, W.J. (2002) BLAT-The BLAST-Like Alignment Tool. Genome Res., 4, 656-664.
16. Li, W. and Godzik, A. (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659. (Pubitemid 43985301)
17. Schroth, G.P. (2011) EMBL-EBI accession no. E-MTAB-513.
18. Trapnell, C., Pachter, L. and Salzberg, S.L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
19. Rossi, D., Rasi, S., Fabbri, G., Spina, V., Fangazio, M., Forconi, F., Marasca, R., Laurenti, L., Bruscaggin, A., Cerri, M. et al. (2012) Mutations of NOTCH1 are an independent predictor of survival in chronic lymphocytic leukemia. Blood, 119, 521-529.
20. Mansur, M.B., Hassan, R., Barbosa, T.C., Splendore, A., Jotta, P.Y., Yunes, J.A., Wiemels, J.L. and Pombo-de-Oliveira, M.S. (2012) Impact of complex NOTCH1 mutations on survival in paediatric T-cell leukemia. BMC Cancer, 12, 9.
21. Futreal, P.A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N. and Stratton, M.R. (2004) A census of human cancer genes. Nat. Rev. Cancer, 4, 177-183. (Pubitemid 38337497)
22. Manske, H.M. and Kwiatkowski, D.P. (2009) SNP-o-matic. Bioinformatics, 25, 2434-2435.
23. Satya, R.V., Zavaljevski, N. and Reifman, J. (2012) A new strategy to reduce allelic bias in RNA-Seq readmapping. Nucleic Acids Res., 40, e127.
24. Bhaduri, A., Qu, K., Lee, C.S., Ungewickell, A. and Khavari, P.A. (2012) Rapid identification of nonhuman sequences in highthroughput sequencing data sets. Bioinformatics, 28, 1174-1175.