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Items: 1 to 20 of 102

1.

Integrated genome sizing (IGS) approach for the parallelization of whole genome analysis.

Sona P, Hong JH, Lee S, Kim BJ, Hong WY, Jung J, Kim HN, Kim HL, Christopher D, Herviou L, Im YH, Lee KY, Kim TS, Jung J.

BMC Bioinformatics. 2018 Dec 3;19(1):462. doi: 10.1186/s12859-018-2499-1.

2.

Group-based variant calling leveraging next-generation supercomputing for large-scale whole-genome sequencing studies.

Standish KA, Carland TM, Lockwood GK, Pfeiffer W, Tatineni M, Huang CC, Lamberth S, Cherkas Y, Brodmerkel C, Jaeger E, Smith L, Rajagopal G, Curran ME, Schork NJ.

BMC Bioinformatics. 2015 Sep 22;16:304. doi: 10.1186/s12859-015-0736-4.

3.

Supercomputing for the parallelization of whole genome analysis.

Puckelwartz MJ, Pesce LL, Nelakuditi V, Dellefave-Castillo L, Golbus JR, Day SM, Cappola TP, Dorn GW 2nd, Foster IT, McNally EM.

Bioinformatics. 2014 Jun 1;30(11):1508-13. doi: 10.1093/bioinformatics/btu071. Epub 2014 Feb 12.

4.

From Wet-Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing.

Laurie S, Fernandez-Callejo M, Marco-Sola S, Trotta JR, Camps J, Chacón A, Espinosa A, Gut M, Gut I, Heath S, Beltran S.

Hum Mutat. 2016 Dec;37(12):1263-1271. doi: 10.1002/humu.23114. Epub 2016 Sep 26.

5.

A Survey of Software and Hardware Approaches to Performing Read Alignment in Next Generation Sequencing.

Al Kawam A, Khatri S, Datta A.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Nov-Dec;14(6):1202-1213. doi: 10.1109/TCBB.2016.2586070. Epub 2016 Jun 29.

PMID:
27362989
6.

Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns.

Comin M, Schimd M.

BMC Bioinformatics. 2014;15 Suppl 9:S1. doi: 10.1186/1471-2105-15-S9-S1. Epub 2014 Sep 10.

7.

PGen: large-scale genomic variations analysis workflow and browser in SoyKB.

Liu Y, Khan SM, Wang J, Rynge M, Zhang Y, Zeng S, Chen S, Maldonado Dos Santos JV, Valliyodan B, Calyam PP, Merchant N, Nguyen HT, Xu D, Joshi T.

BMC Bioinformatics. 2016 Oct 6;17(Suppl 13):337.

8.

Next-generation sequencing: big data meets high performance computing.

Schmidt B, Hildebrandt A.

Drug Discov Today. 2017 Apr;22(4):712-717. doi: 10.1016/j.drudis.2017.01.014. Epub 2017 Feb 2. Review.

PMID:
28163155
9.

Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money.

Vincent AT, Derome N, Boyle B, Culley AI, Charette SJ.

J Microbiol Methods. 2017 Jul;138:60-71. doi: 10.1016/j.mimet.2016.02.016. Epub 2016 Mar 16. Review.

PMID:
26995332
10.

One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies.

Yuan S, Johnston HR, Zhang G, Li Y, Hu YJ, Qin ZS.

PLoS Comput Biol. 2015 Aug 12;11(8):e1004448. doi: 10.1371/journal.pcbi.1004448. eCollection 2015 Aug.

11.

Sequencing technologies and genome sequencing.

Pareek CS, Smoczynski R, Tretyn A.

J Appl Genet. 2011 Nov;52(4):413-35. doi: 10.1007/s13353-011-0057-x. Epub 2011 Jun 23. Review.

12.

Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data.

Liu Y, Hankeln T, Schmidt B.

IEEE/ACM Trans Comput Biol Bioinform. 2016 May-Jun;13(3):592-8. doi: 10.1109/TCBB.2015.2430314.

PMID:
27295644
13.

Coverage bias and sensitivity of variant calling for four whole-genome sequencing technologies.

Rieber N, Zapatka M, Lasitschka B, Jones D, Northcott P, Hutter B, Jäger N, Kool M, Taylor M, Lichter P, Pfister S, Wolf S, Brors B, Eils R.

PLoS One. 2013 Jun 11;8(6):e66621. doi: 10.1371/journal.pone.0066621. Print 2013.

14.

Opportunities and challenges of whole-genome and -exome sequencing.

Petersen BS, Fredrich B, Hoeppner MP, Ellinghaus D, Franke A.

BMC Genet. 2017 Feb 14;18(1):14. doi: 10.1186/s12863-017-0479-5. Review.

15.

SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data.

Peng Y, Maxwell AS, Barker ND, Laird JG, Kennedy AJ, Wang N, Zhang C, Gong P.

BMC Bioinformatics. 2014;15 Suppl 11:S10. doi: 10.1186/1471-2105-15-S11-S10. Epub 2014 Oct 21.

16.

The Genomic Scrapheap Challenge; Extracting Relevant Data from Unmapped Whole Genome Sequencing Reads, Including Strain Specific Genomic Segments, in Rats.

van der Weide RH, Simonis M, Hermsen R, Toonen P, Cuppen E, de Ligt J.

PLoS One. 2016 Aug 8;11(8):e0160036. doi: 10.1371/journal.pone.0160036. eCollection 2016.

17.

RAMBO-K: Rapid and Sensitive Removal of Background Sequences from Next Generation Sequencing Data.

Tausch SH, Renard BY, Nitsche A, Dabrowski PW.

PLoS One. 2015 Sep 17;10(9):e0137896. doi: 10.1371/journal.pone.0137896. eCollection 2015.

18.

NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis.

Singer J, Ruscheweyh HJ, Hofmann AL, Thurnherr T, Singer F, Toussaint NC, Ng CKY, Piscuoglio S, Beisel C, Christofori G, Dummer R, Hall MN, Krek W, Levesque MP, Manz MG, Moch H, Papassotiropoulos A, Stekhoven DJ, Wild P, Wüst T, Rinn B, Beerenwinkel N.

Bioinformatics. 2018 Jan 1;34(1):107-108. doi: 10.1093/bioinformatics/btx540.

19.

Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome.

Faino L, Seidl MF, Datema E, van den Berg GC, Janssen A, Wittenberg AH, Thomma BP.

MBio. 2015 Aug 18;6(4). pii: e00936-15. doi: 10.1128/mBio.00936-15.

20.

Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer.

Peterlongo P, Chikhi R.

BMC Bioinformatics. 2012 Mar 23;13:48. doi: 10.1186/1471-2105-13-48.

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