Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands.
Bioinformatics. 2012 Dec 15;28(24):3225-31. doi: 10.1093/bioinformatics/bts613. Epub 2012 Oct 16.
Metagenomes are often characterized by high levels of unknown sequences. Reads derived from known microorganisms can easily be identified and analyzed using fast homology search algorithms and a suitable reference database, but the unknown sequences are often ignored in further analyses, biasing conclusions. Nevertheless, it is possible to use more data in a comparative metagenomic analysis by creating a cross-assembly of all reads, i.e. a single assembly of reads from different samples. Comparative metagenomics studies the interrelationships between metagenomes from different samples. Using an assembly algorithm is a fast and intuitive way to link (partially) homologous reads without requiring a database of reference sequences.
Here, we introduce crAss, a novel bioinformatic tool that enables fast simple analysis of cross-assembly files, yielding distances between all metagenomic sample pairs and an insightful image displaying the similarities.
宏基因组通常具有高水平的未知序列。使用快速同源搜索算法和合适的参考数据库，可以轻松识别和分析来自已知微生物的读取，但在进一步分析中经常忽略未知序列，从而产生有偏结论。然而，通过创建所有读取的交叉组装（即来自不同样本的读取的单个组装），可以在比较宏基因组分析中使用更多数据。比较宏基因组学研究来自不同样本的宏基因组之间的相互关系。使用组装算法是一种快速直观的方法，可以链接（部分）同源读取，而无需参考序列数据库。
在这里，我们介绍了 crAss，这是一种新的生物信息学工具，可快速简单地分析交叉组装文件，生成所有宏基因组样本对之间的距离以及显示相似性的直观图像。
