Fulcrum: condensing redundant reads from high-throughput sequencing studies

被引：27

作者：

Burriesci, Matthew S. ^{[1
]}

Lehnert, Erik M. ^{[1
]}

Pringle, John R. ^{[1
]}

机构：

[1] Stanford Univ, Dept Genet, Sch Med, Stanford, CA 94305 USA

来源：

BIOINFORMATICS | 2012年 / 28卷 / 10期

基金：

美国国家卫生研究院; 美国国家科学基金会;

关键词：

GENERATION; ERRORS; GENOME;

D O I：

10.1093/bioinformatics/bts123

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Results: We developed Fulcrum to collapse identical and near-identical Illumina and 454 reads (such as those from PCR clones) into single error-corrected sequences; it can process paired-end as well as single-end reads. Fulcrum is customizable and can be deployed on a single machine, a local network or a commercially available MapReduce cluster, and it has been optimized to maximize ease-of-use, cross-platform compatibility and future scalability. Sequence datasets have been collapsed by up to 71%, and the reduced number and improved quality of the resulting sequences allow assemblers to produce longer contigs while using less memory.

引用

页码：1324 / 1327

页数：4

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