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Literature DB >> 25748910

Quality score compression improves genotyping accuracy.

Y William Yu¹, Deniz Yorukoglu², Jian Peng¹, Bonnie Berger¹.

Abstract

Entities: Species

Mesh：

Year: 2015 PMID： 25748910 PMCID： PMC4439189 DOI： 10.1038/nbt.3170

Source DB: PubMed Journal: Nat Biotechnol ISSN： 1087-0156 Impact factor: 54.908

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22 in total

1. Compressive genomics.

Authors: Po-Ru Loh; Michael Baym; Bonnie Berger
Journal: Nat Biotechnol Date: 2012-07-10 Impact factor: 54.908

Review 2. Single-cell sequencing-based technologies will revolutionize whole-organism science.

Authors: Ehud Shapiro; Tamir Biezuner; Sten Linnarsson
Journal: Nat Rev Genet Date: 2013-07-30 Impact factor: 53.242

3. Efficient storage of high throughput DNA sequencing data using reference-based compression.

Authors: Markus Hsi-Yang Fritz; Rasko Leinonen; Guy Cochrane; Ewan Birney
Journal: Genome Res Date: 2011-01-18 Impact factor: 9.043

4. SCALCE: boosting sequence compression algorithms using locally consistent encoding.

Authors: Faraz Hach; Ibrahim Numanagic; Can Alkan; S Cenk Sahinalp
Journal: Bioinformatics Date: 2012-10-09 Impact factor: 6.937

Review 5. Computational solutions for omics data.

Authors: Bonnie Berger; Jian Peng; Mona Singh
Journal: Nat Rev Genet Date: 2013-05 Impact factor: 53.242

6. An integrated map of genetic variation from 1,092 human genomes.

Authors: Goncalo R Abecasis; Adam Auton; Lisa D Brooks; Mark A DePristo; Richard M Durbin; Robert E Handsaker; Hyun Min Kang; Gabor T Marth; Gil A McVean
Journal: Nature Date: 2012-11-01 Impact factor: 49.962

7. QualComp: a new lossy compressor for quality scores based on rate distortion theory.

Authors: Idoia Ochoa; Himanshu Asnani; Dinesh Bharadia; Mainak Chowdhury; Tsachy Weissman; Golan Yona
Journal: BMC Bioinformatics Date: 2013-06-08 Impact factor: 3.169

8. Full-length transcriptome assembly from RNA-Seq data without a reference genome.

Authors: Manfred G Grabherr; Brian J Haas; Moran Yassour; Joshua Z Levin; Dawn A Thompson; Ido Amit; Xian Adiconis; Lin Fan; Raktima Raychowdhury; Qiandong Zeng; Zehua Chen; Evan Mauceli; Nir Hacohen; Andreas Gnirke; Nicholas Rhind; Federica di Palma; Bruce W Birren; Chad Nusbaum; Kerstin Lindblad-Toh; Nir Friedman; Aviv Regev
Journal: Nat Biotechnol Date: 2011-05-15 Impact factor: 54.908

9. Compression of FASTQ and SAM format sequencing data.

Authors: James K Bonfield; Matthew V Mahoney
Journal: PLoS One Date: 2013-03-22 Impact factor: 3.240

10. Compression of next-generation sequencing reads aided by highly efficient de novo assembly.

Authors: Daniel C Jones; Walter L Ruzzo; Xinxia Peng; Michael G Katze
Journal: Nucleic Acids Res Date: 2012-08-16 Impact factor: 16.971

17 in total

Review 1. Towards precision medicine.

Authors: Euan A Ashley
Journal: Nat Rev Genet Date: 2016-08-16 Impact factor: 53.242

Quality score compression improves genotyping accuracy.

1. Compressive genomics.

Review 2. Single-cell sequencing-based technologies will revolutionize whole-organism science.

3. Efficient storage of high throughput DNA sequencing data using reference-based compression.

4. SCALCE: boosting sequence compression algorithms using locally consistent encoding.

Review 5. Computational solutions for omics data.

6. An integrated map of genetic variation from 1,092 human genomes.

7. QualComp: a new lossy compressor for quality scores based on rate distortion theory.

8. Full-length transcriptome assembly from RNA-Seq data without a reference genome.

9. Compression of FASTQ and SAM format sequencing data.

10. Compression of next-generation sequencing reads aided by highly efficient de novo assembly.

Review 1. Towards precision medicine.

2. Effect of lossy compression of quality scores on variant calling.

3. Fast genotyping of known SNPs through approximate k-mer matching.

4. An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values.

5. Entropy-scaling search of massive biological data.

6. CALQ: compression of quality values of aligned sequencing data.

7. The Sequence Read Archive: a decade more of explosive growth.

8. PhredEM: a phred-score-informed genotype-calling approach for next-generation sequencing studies.

9. Computational Biology in the 21st Century: Scaling with Compressive Algorithms.

10. Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph.