In the new issue of Nature Reviews Genetics (Jan 2012) we can read a very interesting and useful review about computational tools for next generation sequencing.
“Rather than describing the algorithmic details of these programs, we will discuss their shared strategies for solving repeat-induced analysis problems in each situation and address some of their limitations” write Todd J. Treangen and Steven L. Salzberg in their introduction.
In this review the authors compile a guide on the challenge represented by the abundance of repeats in genome assembly and RNA-seq analysis. Two list of computational tools are provided, one for NGS genome alignment and assembly, and one for NGS transcriptome analysis.
The range of tools available is wide and grows rapidly, making the analysis of repeats easier, with the ultimate purpose to learn more about their role in disease and their contributions to gene function, genome structure and evolution.
(Figure from the article: Treangen T.J. et al., Nature Gen. Rev. 2012)
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