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Items: 1 to 20 of 382

1.

A beginners guide to SNP calling from high-throughput DNA-sequencing data.

Altmann A, Weber P, Bader D, Preuss M, Binder EB, Müller-Myhsok B.

Hum Genet. 2012 Oct;131(10):1541-54. doi: 10.1007/s00439-012-1213-z. Epub 2012 Aug 11. Review.

PMID:
22886560
2.

WEP: a high-performance analysis pipeline for whole-exome data.

D'Antonio M, D'Onorio De Meo P, Paoletti D, Elmi B, Pallocca M, Sanna N, Picardi E, Pesole G, Castrignanò T.

BMC Bioinformatics. 2013;14 Suppl 7:S11. doi: 10.1186/1471-2105-14-S7-S11. Epub 2013 Apr 22.

3.

Improving mapping and SNP-calling performance in multiplexed targeted next-generation sequencing.

Elsharawy A, Forster M, Schracke N, Keller A, Thomsen I, Petersen BS, Stade B, Stähler P, Schreiber S, Rosenstiel P, Franke A.

BMC Genomics. 2012 Aug 22;13:417. doi: 10.1186/1471-2164-13-417.

4.

Impact of post-alignment processing in variant discovery from whole exome data.

Tian S, Yan H, Kalmbach M, Slager SL.

BMC Bioinformatics. 2016 Oct 3;17(1):403.

5.

Mining SNPs from DNA sequence data; computational approaches to SNP discovery and analysis.

van Oeveren J, Janssen A.

Methods Mol Biol. 2009;578:73-91. doi: 10.1007/978-1-60327-411-1_4.

PMID:
19768587
6.

SNP discovery by transcriptome pyrosequencing.

Barbazuk WB, Schnable PS.

Methods Mol Biol. 2011;729:225-46. doi: 10.1007/978-1-61779-065-2_15.

PMID:
21365494
7.

Analysis of high-throughput sequencing data.

Mane SP, Modise T, Sobral BW.

Methods Mol Biol. 2011;678:1-11. doi: 10.1007/978-1-60761-682-5_1.

PMID:
20931368
8.

Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome.

Azam S, Thakur V, Ruperao P, Shah T, Balaji J, Amindala B, Farmer AD, Studholme DJ, May GD, Edwards D, Jones JD, Varshney RK.

Am J Bot. 2012 Feb;99(2):186-92. doi: 10.3732/ajb.1100419. Epub 2012 Feb 1.

9.

Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey.

Kerstens HH, Crooijmans RP, Veenendaal A, Dibbits BW, Chin-A-Woeng TF, den Dunnen JT, Groenen MA.

BMC Genomics. 2009 Oct 16;10:479. doi: 10.1186/1471-2164-10-479.

10.

Review of alignment and SNP calling algorithms for next-generation sequencing data.

Mielczarek M, Szyda J.

J Appl Genet. 2016 Feb;57(1):71-9. doi: 10.1007/s13353-015-0292-7. Epub 2015 Jun 9. Review.

PMID:
26055432
11.

TotalReCaller: improved accuracy and performance via integrated alignment and base-calling.

Menges F, Narzisi G, Mishra B.

Bioinformatics. 2011 Sep 1;27(17):2330-7. doi: 10.1093/bioinformatics/btr393. Epub 2011 Jun 30.

PMID:
21724593
12.

SNP-PHAGE--High throughput SNP discovery pipeline.

Matukumalli LK, Grefenstette JJ, Hyten DL, Choi IY, Cregan PB, Van Tassell CP.

BMC Bioinformatics. 2006 Oct 23;7:468.

13.

High-throughput identification, database storage and analysis of SNPs in EST sequences.

Useche FJ, Gao G, Harafey M, Rafalski A.

Genome Inform. 2001;12:194-203.

PMID:
11791238
14.

Comparative view of in silico DNA sequencing analysis tools.

Tongsima S, Assawamakin A, Piriyapongsa J, Shaw PJ.

Methods Mol Biol. 2011;760:207-21. doi: 10.1007/978-1-61779-176-5_13.

PMID:
21779999
15.

Mining SNPs from EST sequences using filters and ensemble classifiers.

Wang J, Zou Q, Guo MZ.

Genet Mol Res. 2010 May 4;9(2):820-34. doi: 10.4238/vol9-2gmr765.

16.

ComB: SNP calling and mapping analysis for color and nucleotide space platforms.

Souaiaia T, Frazier Z, Chen T.

J Comput Biol. 2011 Jun;18(6):795-807. doi: 10.1089/cmb.2011.0027. Epub 2011 May 12.

17.

High quality SNP calling using Illumina data at shallow coverage.

Malhis N, Jones SJ.

Bioinformatics. 2010 Apr 15;26(8):1029-35. doi: 10.1093/bioinformatics/btq092. Epub 2010 Feb 26.

PMID:
20190250
18.

A method for discovery of genome-wide SNP between any two genotypes from whole-genome re-sequencing data.

Krishnan SG, Waters DL, Henry RJ.

Methods Mol Biol. 2014;1099:287-94. doi: 10.1007/978-1-62703-715-0_24.

PMID:
24243213
19.

An integrated SNP mining and utilization (ISMU) pipeline for next generation sequencing data.

Azam S, Rathore A, Shah TM, Telluri M, Amindala B, Ruperao P, Katta MA, Varshney RK.

PLoS One. 2014 Jul 8;9(7):e101754. doi: 10.1371/journal.pone.0101754. eCollection 2014.

20.

Validation and assessment of variant calling pipelines for next-generation sequencing.

Pirooznia M, Kramer M, Parla J, Goes FS, Potash JB, McCombie WR, Zandi PP.

Hum Genomics. 2014 Jul 30;8:14. doi: 10.1186/1479-7364-8-14.

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