scholarly journals BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU

PeerJ ◽  
2014 ◽  
Vol 2 ◽  
pp. e421 ◽  
Author(s):  
Ruibang Luo ◽  
Yiu-Lun Wong ◽  
Wai-Chun Law ◽  
Lap-Kei Lee ◽  
Jeanno Cheung ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Secondary Analysis ◽  
Whole Genome ◽  
Whole Exome

scholarly journals BALSA: Integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU

2014 ◽  
Author(s):  
Ruibang Luo ◽  
Yiu-Lun Wong ◽  
Wai-Chun Law ◽  
Lap-Kei Lee ◽  
Chi-Man Liu ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Secondary Analysis ◽  
Variant Calling ◽  
Statistical Testing ◽  
Next Generation Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Accurate Analysis ◽  
Whole Exome

This paper reports an integrated solution, called BALSA, for the secondary analysis of next generation sequencing data; it exploits the computational power of GPU and an intricate memory management to give a fast and accurate analysis. From raw reads to variants (including SNPs and Indels), BALSA, using just a single computing node with a commodity GPU board, takes 5.5 hours to process 50-fold whole genome sequencing (~750 million 100bp paired-end reads), or just 25 minutes for 210-fold whole exome sequencing. BALSA’s speed is rooted at its parallel algorithms to effectively exploit a GPU to speed up processes like alignment, realignment and statistical testing. BALSA incorporates a 16-genotype model to support the calling of SNPs and Indels and achieves competitive variant calling accuracy and sensitivity when compared to the ensemble of six popular variant callers. BALSA also supports efficient identification of somatic SNVs and CNVs; experiments showed that BALSA recovers all the previously validated somatic SNVs and CNVs, and it is more sensitive for somatic Indel detection. BALSA outputs variants in VCF format. A pileup-like SNAPSHOT format, while maintaining the same fidelity as BAM in variant calling, enables efficient storage and indexing, and facilitates the App development of downstream analyses. BALSA is available at: http://sourceforge.net/p/balsa

scholarly journals BALSA: Integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU

2014 ◽  
Author(s):  
Ruibang Luo ◽  
Yiu-Lun Wong ◽  
Wai-Chun Law ◽  
Lap-Kei Lee ◽  
Chi-Man Liu ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Secondary Analysis ◽  
Variant Calling ◽  
Statistical Testing ◽  
Next Generation Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Accurate Analysis ◽  
Whole Exome

This paper reports an integrated solution, called BALSA, for the secondary analysis of next generation sequencing data; it exploits the computational power of GPU and an intricate memory management to give a fast and accurate analysis. From raw reads to variants (including SNPs and Indels), BALSA, using just a single computing node with a commodity GPU board, takes 5.5 hours to process 50-fold whole genome sequencing (~750 million 100bp paired-end reads), or just 25 minutes for 210-fold whole exome sequencing. BALSA’s speed is rooted at its parallel algorithms to effectively exploit a GPU to speed up processes like alignment, realignment and statistical testing. BALSA incorporates a 16-genotype model to support the calling of SNPs and Indels and achieves competitive variant calling accuracy and sensitivity when compared to the ensemble of six popular variant callers. BALSA also supports efficient identification of somatic SNVs and CNVs; experiments showed that BALSA recovers all the previously validated somatic SNVs and CNVs, and it is more sensitive for somatic Indel detection. BALSA outputs variants in VCF format. A pileup-like SNAPSHOT format, while maintaining the same fidelity as BAM in variant calling, enables efficient storage and indexing, and facilitates the App development of downstream analyses. BALSA is available at: http://sourceforge.net/p/balsa

scholarly journals Challenges of using next generation sequencing in newborn screening

2015 ◽  
Vol 97 ◽  
Author(s):  
EYAL REINSTEIN
Keyword(s):  
Newborn Screening ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Ethical Issues ◽  
Whole Genome ◽  
Short Article ◽  
Public Health Programs ◽  
Whole Exome ◽  
Metabolic Conditions ◽  
Widespread Dissemination

SummaryWhole-genome and whole-exome sequencing for clinical applications is now an integral part of medical genetics practice. The term newborn screening refers to public health programs designed to screen newborns for various treatable metabolic conditions, by measuring levels of circulating blood metabolites. The availability and significant decrease in sequencing costs has raised the question of whether metabolic newborn screening should be replaced by whole-genome or whole-exome sequencing. While newborn genome sequencing can potentially increase the number of disorders identified by newborn screening, the generalization of its practice raises a number of important ethical issues. This short article argues that there are medical, psychological, ethical and economic reasons why widespread dissemination of newborn screening is still premature.

scholarly journals Whole-genome sequencing offers additional but limited clinical utility compared with reanalysis of whole-exome sequencing

2018 ◽  
Vol 20 (11) ◽  
pp. 1328-1333 ◽  
Author(s):  
Ahmed Alfares ◽  
Taghrid Aloraini ◽  
Lamia Al subaie ◽  
Abdulelah Alissa ◽  
Ahmed Al Qudsi ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Genome Sequencing ◽  
Clinical Utility ◽  
Whole Genome ◽  
Whole Exome
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