Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2
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- 作者：Nicola Prezza ; Francesco Vezzi ; Max Käller ; Alberto Policriti
- 关键词：Bisulfite ; DNA methylation ; NGS ; Succinct hashing ; BWT
- 刊名：BMC Bioinformatics
- 出版年：2016
- 出版时间：February 2016
- 年：2016
- 卷：17
- 期：4-supp
- 全文大小：884 KB
- 刊物主题：Bioinformatics; Microarrays; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Combinatorial Libraries; Algorithms;
- 出版者：BioMed Central
- ISSN：1471-2105
文摘
Background Bisulfite treatment of DNA followed by sequencing (BS-seq) has become a standard technique in epigenetic studies, providing researchers with tools for generating single-base resolution maps of whole methylomes. Aligning bisulfite-treated reads, however, is a computationally difficult task: bisulfite treatment decreases the (lexical) complexity of low-methylated genomic regions, and C-to-T mismatches may reflect cytosine unmethylation rather than SNPs or sequencing errors. Further challenges arise both during and after the alignment phase: data structures used by the aligner should be fast and should fit into main memory, and the methylation-caller output should be somehow compressed, due to its significant size.