BIMA V3: an aligner customized for mate pair library sequencing

被引：73

作者：

Drucker, Travis M. ^{[1
]}

Johnson, Sarah H. ^{[2
]}

Murphy, Stephen J. ^{[2
]}

Cradic, Kendall W. ^{[3
]}

Therneau, Terry M. ^{[4
]}

Vasmatzis, George ^{[2
]}

机构：

[1] Mayo Clin, Dept Informat Technol, Rochester, MN 55905 USA

[2] Mayo Clin, Dept Mol Med, Rochester, MN 55905 USA

[3] Mayo Clin, Dept Lab Med & Pathol, Rochester, MN 55905 USA

[4] Mayo Clin, Dept Biomed Stat & Informat, Rochester, MN 55905 USA

来源：

BIOINFORMATICS | 2014年 / 30卷 / 11期

关键词：

PROSTATE-CANCER; CELL LYMPHOMAS; ALIGNMENT; DISCOVERY; GENES;

D O I：

10.1093/bioinformatics/btu078

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Mate pair library sequencing is an effective and economical method for detecting genomic structural variants and chromosomal abnormalities. Unfortunately, the mapping and alignment of mate-pair read pairs to a reference genome is a challenging and time-consuming process for most next-generation sequencing alignment programs. Large insert sizes, introduction of library preparation protocol artifacts (biotin junction reads, paired-end read contamination, chimeras, etc.) and presence of structural variant breakpoints within reads increase mapping and alignment complexity. We describe an algorithm that is up to 20 times faster and 25% more accurate than popular next-generation sequencing alignment programs when processing mate pair sequencing.

引用

页码：1627 / 1629

页数：3

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