Evaluating the quality of metagenome assemblies can be a challenging task, especially when no reference genome is available and when comparing samples at various taxonomic complexity and sequencing depth. A high quality assembly is expected not only to produce high quality bins, but also to be representative of most of the read sequences, especially in complex samples where algorithms struggle reconstructing low-abundance genomes. Recent studies showed a great improvement in number and quality of bins obtained with highly accurate PacBio HiFi long reads. It remains however to be assessed how much of the sample these bins represent, especially in highly complex environmental samples. There is therefore a need to use and compare other evaluation methods. We designed and implemented Mapler, a metagenomic assembly and evaluation pipeline with a primary focus on evaluating the quality of HiFi-based metagenome assemblies. It incorporates state-of-the-art tools for assembly, binning, and assembly evaluation. In addition to classifying assembly bins in classical quality categories according to their marker gene content and taxonomic assignment, Mapler analyzes the alignment of reads on contigs. To do so, it calculates the ratio of mapped reads and bases, and separately analyzes mapped and unmapped reads via their k-mer frequency, read quality, and taxonomic assignment.Read less <