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BMC Genomics. 2017 Oct 3;18(Suppl 6):691. doi: 10.1186/s12864-017-4021-y.

SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads.

Author information

1
Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. Oliver.Hampton@bcm.edu.
2
Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. Oliver.Hampton@bcm.edu.
3
Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
4
Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
5
Department of Pediatrics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
6
Texas Children's Hospital, 6621 Fanin Street, Houston, TX, 77030, USA.

Abstract

BACKGROUND:

Characterization of genomic structural variation (SV) is essential to expanding the research and clinical applications of genome sequencing. Reliance upon short DNA fragment paired end sequencing has yielded a wealth of single nucleotide variants and internal sequencing read insertions-deletions, at the cost of limited SV detection. Multi-kilobase DNA fragment mate pair sequencing has supplemented the void in SV detection, but introduced new analytic challenges requiring SV detection tools specifically designed for mate pair sequencing data. Here, we introduce SVachra - Structural Variation Assessment of CHRomosomal Aberrations, a breakpoint calling program that identifies large insertions-deletions, inversions, inter- and intra-chromosomal translocations utilizing both inward and outward facing read types generated by mate pair sequencing.

RESULTS:

We demonstrate SVachra's utility by executing the program on large-insert (Illumina Nextera) mate pair sequencing data from the personal genome of a single subject (HS1011). An additional data set of long-read (Pacific BioSciences RSII) was also generated to validate SV calls from SVachra and other comparison SV calling programs. SVachra exhibited the highest validation rate and reported the widest distribution of SV types and size ranges when compared to other SV callers.

CONCLUSIONS:

SVachra is a highly specific breakpoint calling program that exhibits a more unbiased SV detection methodology than other callers.

KEYWORDS:

Breakpoint discovery; Mate pair sequencing; Structural variation

PMID:
28984202
PMCID:
PMC5629590
DOI:
10.1186/s12864-017-4021-y
[Indexed for MEDLINE]
Free PMC Article

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