Motivation High-throughput next-generation sequencing can generate huge sequence files, whose analysis requires alignment algorithms that are typically very demanding in terms of memory and computational resources. This is a significant issue, especially for machines with limited hardware capabilities. As the redundancy of the sequences typically increases with coverage, collapsing such files into compact sets of non-redundant reads has the 2-fold advantage of reducing file size and speeding-up the alignment, avoiding to map the same sequence multiple times. Method BioSeqZip generates compact and sorted lists of alignment-ready non-redundant sequences, keeping track of their occurrences in the raw files as well as of their quality score information. By exploiting a memory-constrained external sorting algorithm, it can be executed on either single- or multi-sample datasets even on computers with medium computational capabilities. On request, it can even re-expand the compacted files to their original state. Results Our extensive experiments on RNA-Seq data show that BioSeqZip considerably brings down the computational costs of a standard sequence analysis pipeline, with particular benefits for the alignment procedures that typically have the highest requirements in terms of memory and execution time. In our tests, BioSeqZip was able to compact 2.7 billion of reads into 963 million of unique tags reducing the size of sequence files up to 70% and speeding-up the alignment by 50% at least. Availability and implementation BioSeqZip is available at https://github.com/bioinformatics-polito/BioSeqZip. Supplementary information Supplementary data are available at Bioinformatics online.

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In this work, we present an innovative approach for damage detection of infrastructures on-edge devices, exploiting a brain-inspired algorithm. The proposed solution exploits recurrent spiking neural networks (LSNNs), which are emerging for their theoretical energy efficiency and compactness, to recognise damage conditions by processing data from low-cost accelerometers (MEMS) directly on the sensor node. We focus on designing an efficient coding of MEMS data to optimise SNN execution on a low-power microcontroller. We characterised and profiled LSNN performance and energy consumption on a hardware prototype sensor node equipped with an STM32 embedded microcontroller and a digital MEMS accelerometer. We used a hardware-in-the-loop environment with virtual sensors generating data on an SPI interface connected to the physical microcontroller to evaluate the system with a data stream from a real viaduct. We exploited this environment also to study the impact of different on-sensor encoding techniques, mimicking a bio-inspired sensor able to generate events instead of accelerations. Obtained results show that the proposed optimised embedded LSNN (eLSNN), when using a spike-based input encoding technique, achieves 54% lower execution time with respect to a naive LSNN algorithm implementation present in the state-of-the-art. The optimised eLSNN requires around 47 kCycles, which is comparable with the data transfer cost from the SPI interface. However, the spike-based encoding technique requires considerably larger input vectors to get the same classification accuracy, resulting in a longer pre-processing and sensor access time. Overall the event-based encoding techniques leads to a longer execution time (1.49×) but similar energy consumption. Moving this coding on the sensor can remove this limitation leading to an overall more energy-efficient monitoring system.