MAIRA - Highly efficient and accurate algorithms for mobile analysis of microbes

生物信息学是一个由技术驱动的研究领域，移动测序是一个令人兴奋的新技术发展。这是基于牛津纳米孔的奴才。这是一个执行单分子测序的小型USB设备。移动测序将极大地减少从样本采集到完成测序的时间，并允许测序进入现场，从而打开许多新的研究机会。该项目的目标是开发一套新的算法，对微生物进行高效和准确的移动分析。一旦序列的第一个碱基开始以在线方式出现在移动测序仪上，算法就会分析序列，并就样本的微生物含量提供早期反馈。这些算法将通过对检测到的基因内容进行仔细分析，寻求识别微生物，直到菌株水平。一个关键问题是对已知微生物的大型数据库执行快速比对读取。这将使用最先进的算法技术来解决，例如所谓的双重索引和间隔种子。应变水平识别是一个困难的问题，将开发新的算法来解决这一问题。新的算法将在一个名为Maira的计算机程序中使用，Maira是使用快速算法进行微生物识别的首字母缩写。

Bioinformatics is a technology-driven research area and a new exciting technological development is mobile sequencing. This is based on the Oxford Nanopore MinION. This is a small USB device that performs single molecule sequencing. Mobile sequencing will open many new research opportunities by greatly reducing the time from sample collection to completed sequencing, and by allowing sequencing to be taken into the field. The aim of this project is to develop a suite of new algorithms that perform highly efficient and accurate mobile analysis of microbes. The algorithms will analyze sequences as soon as their first bases start coming of the mobile sequencer in an online fashion, giving early feedback on the microbial content of a sample. The algorithms will seek to identify microbes down to the strain-level by performing a careful analysis of the detected gene content. A key problem is to perform a fast alignment of reads against a large database of known microbes. This will be addressed using state-of-the-art algorithmic techniques such as so-called double indexing and spaced seeds. Strain-level identification is a difficult problem and new algorithms will be developed to address this. The new algorithms will be made available in a computer program called MAIRA, an acronym for microbe identification using rapid algorithms.