Literature DB >> 28916731

Need for speed in accurate whole-genome data analysis: GENALICE MAP challenges BWA/GATK more than PEMapper/PECaller and Isaac.

Michel Plüss1,2, Anna M Kopps1, Irene Keller3, Janine Meienberg1, Sylvan M Caspar1, Nicolo Dubacher1, Rémy Bruggmann4, Manfred Vogel2, Gabor Matyas5,6.   

Abstract

Mesh:

Year:  2017        PMID: 28916731      PMCID: PMC5635930          DOI: 10.1073/pnas.1713830114

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


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  8 in total

1.  Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms.

Authors:  Come Raczy; Roman Petrovski; Christopher T Saunders; Ilya Chorny; Semyon Kruglyak; Elliott H Margulies; Han-Yu Chuang; Morten Källberg; Swathi A Kumar; Arnold Liao; Kristina M Little; Michael P Strömberg; Stephen W Tanner
Journal:  Bioinformatics       Date:  2013-06-04       Impact factor: 6.937

2.  Compressive mapping for next-generation sequencing.

Authors:  Deniz Yorukoglu; Yun William Yu; Jian Peng; Bonnie Berger
Journal:  Nat Biotechnol       Date:  2016-04       Impact factor: 54.908

3.  Extensive sequencing of seven human genomes to characterize benchmark reference materials.

Authors:  Justin M Zook; David Catoe; Jennifer McDaniel; Lindsay Vang; Noah Spies; Arend Sidow; Ziming Weng; Yuling Liu; Christopher E Mason; Noah Alexander; Elizabeth Henaff; Alexa B R McIntyre; Dhruva Chandramohan; Feng Chen; Erich Jaeger; Ali Moshrefi; Khoa Pham; William Stedman; Tiffany Liang; Michael Saghbini; Zeljko Dzakula; Alex Hastie; Han Cao; Gintaras Deikus; Eric Schadt; Robert Sebra; Ali Bashir; Rebecca M Truty; Christopher C Chang; Natali Gulbahce; Keyan Zhao; Srinka Ghosh; Fiona Hyland; Yutao Fu; Mark Chaisson; Chunlin Xiao; Jonathan Trow; Stephen T Sherry; Alexander W Zaranek; Madeleine Ball; Jason Bobe; Preston Estep; George M Church; Patrick Marks; Sofia Kyriazopoulou-Panagiotopoulou; Grace X Y Zheng; Michael Schnall-Levin; Heather S Ordonez; Patrice A Mudivarti; Kristina Giorda; Ying Sheng; Karoline Bjarnesdatter Rypdal; Marc Salit
Journal:  Sci Data       Date:  2016-06-07       Impact factor: 6.444

Review 4.  Toward better understanding of artifacts in variant calling from high-coverage samples.

Authors:  Heng Li
Journal:  Bioinformatics       Date:  2014-06-27       Impact factor: 6.937

5.  Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.

Authors:  Justin M Zook; Brad Chapman; Jason Wang; David Mittelman; Oliver Hofmann; Winston Hide; Marc Salit
Journal:  Nat Biotechnol       Date:  2014-02-16       Impact factor: 54.908

6.  From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.

Authors:  Geraldine A Van der Auwera; Mauricio O Carneiro; Christopher Hartl; Ryan Poplin; Guillermo Del Angel; Ami Levy-Moonshine; Tadeusz Jordan; Khalid Shakir; David Roazen; Joel Thibault; Eric Banks; Kiran V Garimella; David Altshuler; Stacey Gabriel; Mark A DePristo
Journal:  Curr Protoc Bioinformatics       Date:  2013

7.  PEMapper and PECaller provide a simplified approach to whole-genome sequencing.

Authors:  H Richard Johnston; Pankaj Chopra; Thomas S Wingo; Viren Patel; Michael P Epstein; Jennifer G Mulle; Stephen T Warren; Michael E Zwick; David J Cutler
Journal:  Proc Natl Acad Sci U S A       Date:  2017-02-21       Impact factor: 11.205

8.  Clinical sequencing: is WGS the better WES?

Authors:  Janine Meienberg; Rémy Bruggmann; Konrad Oexle; Gabor Matyas
Journal:  Hum Genet       Date:  2016-01-07       Impact factor: 4.132

  8 in total
  10 in total

1.  Reply to Plüss et al.: The strength of PEMapper/PECaller lies in unbiased calling using large sample sizes.

Authors:  H Richard Johnston; Pankaj Chopra; Thomas S Wingo; Viren Patel; Michael P Epstein; Jennifer G Mulle; Stephen T Warren; Michael E Zwick; David J Cutler
Journal:  Proc Natl Acad Sci U S A       Date:  2017-09-15       Impact factor: 11.205

2.  Widespread genetic heterogeneity of human ribosomal RNA genes.

Authors:  Wenjun Fan; Eetu Eklund; Rachel M Sherman; Hester Liu; Stephanie Pitts; Brittany Ford; N V Rajeshkumar; Marikki Laiho
Journal:  RNA       Date:  2022-02-02       Impact factor: 4.942

3.  A characterization of postzygotic mutations identified in monozygotic twins.

Authors:  Klaasjan G Ouwens; Rick Jansen; Bas Tolhuis; P Eline Slagboom; Brenda W J H Penninx; Dorret I Boomsma
Journal:  Hum Mutat       Date:  2018-07-18       Impact factor: 4.878

4.  elPrep 4: A multithreaded framework for sequence analysis.

Authors:  Charlotte Herzeel; Pascal Costanza; Dries Decap; Jan Fostier; Wilfried Verachtert
Journal:  PLoS One       Date:  2019-02-13       Impact factor: 3.240

5.  Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy.

Authors:  Katherine I Kendig; Saurabh Baheti; Matthew A Bockol; Travis M Drucker; Steven N Hart; Jacob R Heldenbrand; Mikel Hernaez; Matthew E Hudson; Michael T Kalmbach; Eric W Klee; Nathan R Mattson; Christian A Ross; Morgan Taschuk; Eric D Wieben; Mathieu Wiepert; Derek E Wildman; Liudmila S Mainzer
Journal:  Front Genet       Date:  2019-08-20       Impact factor: 4.599

6.  Recommendations for performance optimizations when using GATK3.8 and GATK4.

Authors:  Jacob R Heldenbrand; Saurabh Baheti; Matthew A Bockol; Travis M Drucker; Steven N Hart; Matthew E Hudson; Ravishankar K Iyer; Michael T Kalmbach; Katherine I Kendig; Eric W Klee; Nathan R Mattson; Eric D Wieben; Mathieu Wiepert; Derek E Wildman; Liudmila S Mainzer
Journal:  BMC Bioinformatics       Date:  2019-11-08       Impact factor: 3.169

7.  GTX.Digest.VCF: an online NGS data interpretation system based on intelligent gene ranking and large-scale text mining.

Authors:  Yanhuang Jiang; Chengkun Wu; Yanghui Zhang; Shaowei Zhang; Shuojun Yu; Peng Lei; Qin Lu; Yanwei Xi; Hua Wang; Zhuo Song
Journal:  BMC Med Genomics       Date:  2019-12-20       Impact factor: 3.063

8.  Variant filtering, digenic variants, and other challenges in clinical sequencing: a lesson from fibrillinopathies.

Authors:  Arash Najafi; Sylvan M Caspar; Janine Meienberg; Marianne Rohrbach; Beat Steinmann; Gabor Matyas
Journal:  Clin Genet       Date:  2019-10-01       Impact factor: 4.438

9.  Added Value of Clinical Sequencing: WGS-Based Profiling of Pharmacogenes.

Authors:  Sylvan M Caspar; Timo Schneider; Janine Meienberg; Gabor Matyas
Journal:  Int J Mol Sci       Date:  2020-03-26       Impact factor: 5.923

10.  CNV Radar: an improved method for somatic copy number alteration characterization in oncology.

Authors:  David Soong; Jeran Stratford; Herve Avet-Loiseau; Nizar Bahlis; Faith Davies; Angela Dispenzieri; A Kate Sasser; Jordan M Schecter; Ming Qi; Chad Brown; Wendell Jones; Jonathan J Keats; Daniel Auclair; Christopher Chiu; Jason Powers; Michael Schaffer
Journal:  BMC Bioinformatics       Date:  2020-03-06       Impact factor: 3.169

  10 in total

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