Clustering of reads with alignment-free measures and quality values

BACKGROUND: The data volume generated by Next-Generation Sequencing (NGS) technologies is growing at a pace that is now challenging the storage and data processing capacities of modern computer systems. In this context an important aspect is the reduction of data complexity by collapsing redundant reads in a single cluster to improve the run time, memory requirements, and quality of post-processing steps like assembly and error correction. Several alignment-free measures, based on k-mers counts, have been used to cluster reads. Quality scores produced by NGS platforms are fundamental for various analysis of NGS data like reads mapping and error detection. Moreover future-generation sequencing platforms will produce long reads but with a large number of erroneous bases (up to 15 %). RESULTS: In this scenario it will be fundamental to exploit quality value information within the alignment-free framework. To the best of our knowledge this is the first study that incorporates quality value information and k-mers counts, in the context of alignment-free measures, for the comparison of reads data. Based on this principles, in this paper we present a family of alignment-free measures called D(q)-type. A set of experiments on simulated and real reads data confirms that the new measures are superior to other classical alignment-free statistics, especially when erroneous reads are considered. Also results on de novo assembly and metagenomic reads classification show that the introduction of quality values improves over standard alignment-free measures. These statistics are implemented in a software called QCluster (http://www.dei.unipd.it/~ciompin/main/qcluster.html)

Next Generation Cloud Computing: New Trends and Research Directions

The landscape of cloud computing has significantly changed over the last decade. Not only have more providers and service offerings crowded the space, but also cloud infrastructure that was traditionally limited to single provider data centers is now evolving. In this paper, we firstly discuss the changing cloud infrastructure and consider the use of infrastructure from multiple providers and the benefit of decentralising computing away from data centers. These trends have resulted in the need for a variety of new computing architectures that will be offered by future cloud infrastructure. These architectures are anticipated to impact areas, such as connecting people and devices, data-intensive computing, the service space and self-learning systems. Finally, we lay out a roadmap of challenges that will need to be addressed for realising the potential of next generation cloud systems.Comment: Accepted to Future Generation Computer Systems, 07 September 201