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Items: 1 to 20 of 315


INDELseek: detection of complex insertions and deletions from next-generation sequencing data.

Au CH, Leung AY, Kwong A, Chan TL, Ma ES.

BMC Genomics. 2017 Jan 5;18(1):16. doi: 10.1186/s12864-016-3449-9.


mInDel: a high-throughput and efficient pipeline for genome-wide InDel marker development.

Lv Y, Liu Y, Zhao H.

BMC Genomics. 2016 Apr 14;17:290. doi: 10.1186/s12864-016-2614-5.


SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations.

Liu Y, Loewer M, Aluru S, Schmidt B.

BMC Syst Biol. 2016 Aug 1;10 Suppl 2:47. doi: 10.1186/s12918-016-0300-5.


Optimized detection of insertions/deletions (INDELs) in whole-exome sequencing data.

Kim BY, Park JH, Jo HY, Koo SK, Park MH.

PLoS One. 2017 Aug 9;12(8):e0182272. doi: 10.1371/journal.pone.0182272. eCollection 2017.


Evaluation and optimisation of indel detection workflows for ion torrent sequencing of the BRCA1 and BRCA2 genes.

Yeo ZX, Wong JC, Rozen SG, Lee AS.

BMC Genomics. 2014 Jun 24;15:516. doi: 10.1186/1471-2164-15-516.


Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations.

Sun Z, Bhagwate A, Prodduturi N, Yang P, Kocher JA.

Brief Bioinform. 2017 Nov 1;18(6):973-983. doi: 10.1093/bib/bbw069.


Amplicon Indel Hunter Is a Novel Bioinformatics Tool to Detect Large Somatic Insertion/Deletion Mutations in Amplicon-Based Next-Generation Sequencing Data.

Kadri S, Zhen CJ, Wurst MN, Long BC, Jiang ZF, Wang YL, Furtado LV, Segal JP.

J Mol Diagn. 2015 Nov;17(6):635-43. doi: 10.1016/j.jmoldx.2015.06.005. Epub 2015 Aug 28. Erratum in: J Mol Diagn. 2017 May;19(3):485.


Vindel: a simple pipeline for checking indel redundancy.

Li Z, Wu X, He B, Zhang L.

BMC Bioinformatics. 2014 Nov 19;15:359. doi: 10.1186/s12859-014-0359-1.


An analytical workflow for accurate variant discovery in highly divergent regions.

Tian S, Yan H, Neuhauser C, Slager SL.

BMC Genomics. 2016 Sep 2;17:703. doi: 10.1186/s12864-016-3045-z.


VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research.

Lai Z, Markovets A, Ahdesmaki M, Chapman B, Hofmann O, McEwen R, Johnson J, Dougherty B, Barrett JC, Dry JR.

Nucleic Acids Res. 2016 Jun 20;44(11):e108. doi: 10.1093/nar/gkw227. Epub 2016 Apr 7.


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.


ABRA: improved coding indel detection via assembly-based realignment.

Mose LE, Wilkerson MD, Hayes DN, Perou CM, Parker JS.

Bioinformatics. 2014 Oct;30(19):2813-5. doi: 10.1093/bioinformatics/btu376. Epub 2014 Jun 6.


A study on fast calling variants from next-generation sequencing data using decision tree.

Li Z, Wang Y, Wang F.

BMC Bioinformatics. 2018 Apr 19;19(1):145. doi: 10.1186/s12859-018-2147-9.


Evaluating the Calling Performance of a Rare Disease NGS Panel for Single Nucleotide and Copy Number Variants.

Cacheiro P, Ordóñez-Ugalde A, Quintáns B, Piñeiro-Hermida S, Amigo J, García-Murias M, Pascual-Pascual SI, Grandas F, Arpa J, Carracedo A, Sobrido MJ.

Mol Diagn Ther. 2017 Jun;21(3):303-313. doi: 10.1007/s40291-017-0268-x.


CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting.

Münz M, Ruark E, Renwick A, Ramsay E, Clarke M, Mahamdallie S, Cloke V, Seal S, Strydom A, Lunter G, Rahman N.

Genome Med. 2015 Jul 28;7:76. doi: 10.1186/s13073-015-0195-6.


ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly.

Yang R, Nelson AC, Henzler C, Thyagarajan B, Silverstein KA.

Genome Med. 2015 Dec 7;7:127. doi: 10.1186/s13073-015-0251-2.


HeurAA: accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.

Pongor LS, Pintér F, Peták I.

PLoS One. 2013;8(1):e54294. doi: 10.1371/journal.pone.0054294. Epub 2013 Jan 18.


Comparison of insertion/deletion calling algorithms on human next-generation sequencing data.

Ghoneim DH, Myers JR, Tuttle E, Paciorkowski AR.

BMC Res Notes. 2014 Dec 1;7:864. doi: 10.1186/1756-0500-7-864.


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.


Indel variant analysis of short-read sequencing data with Scalpel.

Fang H, Bergmann EA, Arora K, Vacic V, Zody MC, Iossifov I, O'Rawe JA, Wu Y, Jimenez Barron LT, Rosenbaum J, Ronemus M, Lee YH, Wang Z, Dikoglu E, Jobanputra V, Lyon GJ, Wigler M, Schatz MC, Narzisi G.

Nat Protoc. 2016 Dec;11(12):2529-2548. doi: 10.1038/nprot.2016.150. Epub 2016 Nov 17.

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