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Items: 1 to 20 of 80

1.

Tracking the NGS revolution: managing life science research on shared high-performance computing clusters.

Dahlö M, Scofield DG, Schaal W, Spjuth O.

Gigascience. 2018 May 1;7(5). doi: 10.1093/gigascience/giy028.

2.

NEAT: a framework for building fully automated NGS pipelines and analyses.

Schorderet P.

BMC Bioinformatics. 2016 Feb 1;17:53. doi: 10.1186/s12859-016-0902-3.

3.

Recommendations on e-infrastructures for next-generation sequencing.

Spjuth O, Bongcam-Rudloff E, Dahlberg J, Dahlö M, Kallio A, Pireddu L, Vezzi F, Korpelainen E.

Gigascience. 2016 Jun 7;5:26. doi: 10.1186/s13742-016-0132-7. Review.

4.

Colib'read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads.

Le Bras Y, Collin O, Monjeaud C, Lacroix V, Rivals É, Lemaitre C, Miele V, Sacomoto G, Marchet C, Cazaux B, Zine El Aabidine A, Salmela L, Alves-Carvalho S, Andrieux A, Uricaru R, Peterlongo P.

Gigascience. 2016 Feb 11;5:9. doi: 10.1186/s13742-015-0105-2. eCollection 2016.

5.

A comparative study of k-spectrum-based error correction methods for next-generation sequencing data analysis.

Akogwu I, Wang N, Zhang C, Gong P.

Hum Genomics. 2016 Jul 25;10 Suppl 2:20. doi: 10.1186/s40246-016-0068-0.

6.

NGS-FC: A Next-Generation Sequencing Data Format Converter.

Chunjiang Yu, Wentao Wu, Jing Wang, Yuxin Lin, Yang Yang, Jiajia Chen, Fei Zhu, Bairong Shen.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Sep-Oct;15(5):1683-1691. doi: 10.1109/TCBB.2017.2722442. Epub 2017 Jul 3.

PMID:
28682264
7.

FDA's Activities Supporting Regulatory Application of "Next Gen" Sequencing Technologies.

Wilson CA, Simonyan V.

PDA J Pharm Sci Technol. 2014 Nov-Dec;68(6):626-30. doi: 10.5731/pdajpst.2014.01024.

PMID:
25475637
8.

Leveraging the power of high performance computing for next generation sequencing data analysis: tricks and twists from a high throughput exome workflow.

Kawalia A, Motameny S, Wonczak S, Thiele H, Nieroda L, Jabbari K, Borowski S, Sinha V, Gunia W, Lang U, Achter V, Nürnberg P.

PLoS One. 2015 May 5;10(5):e0126321. doi: 10.1371/journal.pone.0126321. eCollection 2015.

9.

Analysis of next-generation sequencing data using Galaxy.

Blankenberg D, Hillman-Jackson J.

Methods Mol Biol. 2014;1150:21-43. doi: 10.1007/978-1-4939-0512-6_2.

PMID:
24743989
10.

SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis.

Hatakeyama M, Opitz L, Russo G, Qi W, Schlapbach R, Rehrauer H.

BMC Bioinformatics. 2016 Jun 2;17(1):228. doi: 10.1186/s12859-016-1104-8.

11.

ASEQ: fast allele-specific studies from next-generation sequencing data.

Romanel A, Lago S, Prandi D, Sboner A, Demichelis F.

BMC Med Genomics. 2015 Mar 1;8:9. doi: 10.1186/s12920-015-0084-2.

12.

CANEapp: a user-friendly application for automated next generation transcriptomic data analysis.

Velmeshev D, Lally P, Magistri M, Faghihi MA.

BMC Genomics. 2016 Jan 13;17:49. doi: 10.1186/s12864-015-2346-y.

13.

Secure and robust cloud computing for high-throughput forensic microsatellite sequence analysis and databasing.

Bailey SF, Scheible MK, Williams C, Silva DSBS, Hoggan M, Eichman C, Faith SA.

Forensic Sci Int Genet. 2017 Nov;31:40-47. doi: 10.1016/j.fsigen.2017.08.008. Epub 2017 Aug 8.

PMID:
28837856
14.
15.

Anatomy of BioJS, an open source community for the life sciences.

Yachdav G, Goldberg T, Wilzbach S, Dao D, Shih I, Choudhary S, Crouch S, Franz M, García A, García LJ, Grüning BA, Inupakutika D, Sillitoe I, Thanki AS, Vieira B, Villaveces JM, Schneider MV, Lewis S, Pettifer S, Rost B, Corpas M.

Elife. 2015 Jul 8;4. doi: 10.7554/eLife.07009.

16.

Next-generation sequencing and large genome assemblies.

Henson J, Tischler G, Ning Z.

Pharmacogenomics. 2012 Jun;13(8):901-15. doi: 10.2217/pgs.12.72. Review.

17.

QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation.

Wagle P, Nikolić M, Frommolt P.

BMC Genomics. 2015 Jul 1;16:487. doi: 10.1186/s12864-015-1695-x.

18.

Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot.

Loh YH, Shen L.

Methods Mol Biol. 2016;1415:371-83. doi: 10.1007/978-1-4939-3572-7_18.

PMID:
27115642
19.

Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data.

Hermida L, Poussin C, Stadler MB, Gubian S, Sewer A, Gaidatzis D, Hotz HR, Martin F, Belcastro V, Cano S, Peitsch MC, Hoeng J.

BMC Genomics. 2013 Jul 29;14:514. doi: 10.1186/1471-2164-14-514.

20.

STINGRAY: system for integrated genomic resources and analysis.

Wagner G, Jardim R, Tschoeke DA, Loureiro DR, Ocaña KA, Ribeiro AC, Emmel VE, Probst CM, Pitaluga AN, Grisard EC, Cavalcanti MC, Campos ML, Mattoso M, Dávila AM.

BMC Res Notes. 2014 Mar 7;7:132. doi: 10.1186/1756-0500-7-132.

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