MOTIVATION: The k-mer frequency in whole genome sequences provides researchers with an insightful perspective on genomic complexity, comparative genomics, metagenomics and phylogeny. The current k-mer counting tools are typically slow, and they require large memory and hard disk for assembled genome analysis. RESULTS: We propose a novel and ultra-fast k-mer counting algorithm, KCOSS, to fulfill k-mer counting mainly for assembled genomes with segmented Bloom filter, lock-free queue, lock-free thread pool and cuckoo hash table. We optimize running time and memory consumption by recycling memory blocks, merging multiple consecutive first-occurrence k-mers into C-read, and writing a set of C-reads to disk asynchronously. KCOSS was comparatively tested with Jellyfish2, CHTKC and KMC3 on seven assembled genomes and three sequencing datasets in running time, memory consumption, and hard disk occupation. The experimental results show that KCOSS counts k-mer with less memory and disk while having a shorter running time on assembled genomes. KCOSS can be used to calculate the k-mer frequency not only for assembled genomes but also for sequencing data. AVAILABILITYAND IMPLEMENTATION: The KCOSS software is implemented in C++. It is freely available on GitHub: https://github.com/kcoss-2021/KCOSS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Underwater acoustic sensor networks (UASNs) currently provide an important technical means of underwater communication, but there are difficulties in power updating or power replenishment because the sensor nodes work in an underwater environment. Therefore, energy consumption optimization has become the focus of research on UASNs. Node clustering is widely considered to be able to optimize network energy consumption. Although the current clustering-based routing method prolongs the network life cycle to a certain extent, some nodes may fail due to excessive energy consumption caused by excessive data transmission tasks, and the problems of high and uneven energy consumption still exist. To extend the life cycle of UASNs, this article proposes an unequal clustering method based on particle swarm optimization. Our method uses iterative updates to dynamically adjust the cluster size based on the remaining energy of the cluster head, the distance from the cluster head to the Sink node, and the number of times the cluster head forwards data between clusters to balance the cluster head load. The energy consumption of the whole path from the cluster head to the Sink node and the number of hops required are considered in the intercluster transmission phase. Simulation results show that this method can effectively reduce the network energy consumption.