Although current long-read sequencing technologies have a long-read length that facilitates assembly for genome reconstruction, they have high sequence errors. While various assemblers with different perspectives have been developed, no systematic evaluation of assemblers with long reads for diploid genomes with varying heterozygosity has been performed. Here, we evaluated a series of processes, including the estimation of genome characteristics such as genome size and heterozygosity, de novo assembly, polishing, and removal of allelic contigs, using six genomes with various heterozygosity levels. We evaluated five long-read-only assemblers (Canu, Flye, miniasm, NextDenovo and Redbean) and five hybrid assemblers that combine short and long reads (HASLR, MaSuRCA, Platanus-allee, SPAdes and WENGAN) and proposed a concrete guideline for the construction of haplotype representation according to the degree of heterozygosity, followed by polishing and purging haplotigs, using stable and high-performance assemblers: Redbean, Flye and MaSuRCA.

The world is on the cusp of a post-antibiotic period. A century ago, before the advent of antibiotics, bacteriophage therapy was the treatment of choice for bacterial infections. Although bacteriophages have yet to be approved as a treatment in Western medicine, researchers and clinicians have begun to anticipate phage therapy. Bacteriophages are viruses that depend on bacterial cell metabolism to multiply. They offer a promising alternative to the use of antibiotics and an excellent antibacterial option for combating multidrug resistance in bacteria. However, not every phage is suitable for phage therapy. In particular, prophages should not be used because they can lysogenize host cells instead of lysing them. To offer adequate therapeutic options for patients suffering from various infectious diseases, a wide selection of different phages is needed. While there is no evidence of direct toxicity induced by phage particles, it is crucial to study mammalian cell-phage interactions. This requires phage preparations to be free of bacterial cells, toxins and other compounds to avoid skewing host responses. Negative staining of purified viruses and electron microscopy remain the gold standard in the identification of bacteriophages. Interestingly, genomics has greatly changed our understanding of phage biology. Bacteriophage genome sequencing is essential to obtain a complete understanding of the bacteriophages\' biology and to obtain confirmation of their lifestyle. Full genetic sequencing of bacteriophage will enable a better understanding of the phage-encoded proteins and biomolecules (especially phage lytic enzymes) involved in the process of bacterial cell lysis and death. Mass spectrometry can be used for the identification of phage structural proteins. The use of lytic phages as biocontrol agents requires the most appropriate and standard methods to ensure application safety. This review pursues recent research and methods in molecular biology for the isolation and characterization of phages to facilitate follow-up and implementation of work for other researchers. Patents related to this topic have been mentioned in the text.

OBJECTIVE: Next Generation Sequencing (NGS) is increasingly used for the diagnosis of rare genetic disorders. The aim of this study is to review the different approaches for economic evaluations of Next Generation Sequencing (NGS) in pediatric care used to date, to identify all costs, effects, and time horizons taken into account.
METHODS: A systematic literature review was conducted to identify published economic evaluations of NGS applications in pediatric diagnostics, i.e. exome sequencing (ES) and/or genome sequencing (GS). Information regarding methodological approach, costs, effects, and time horizon was abstracted from these publications.
RESULTS: Twenty-eight economic evaluations of ES/GS within pediatrics were identified. Costs included were mainly restricted to direct in-hospital healthcare costs and varied widely in inclusion of sort of costs and time-horizon. Nineteen studies included diagnostic yield and eight studies included cost-effectiveness as outcome measures. Studies varied greatly in terms of included sort of costs data, effects, and time horizon.
CONCLUSIONS: Large differences in inclusion of cost and effect parameters were identified between studies. Validity of outcomes can therefore be questioned, which hinders valid comparison and widespread generalization of conclusions. In addition to current health economic guidance, specific guidance for evaluations in pediatric care is therefore necessary to improve the validity of outcomes and furthermore facilitate comparable decision-making for implementing novel NGS-based diagnostic modalities in pediatric genetics and beyond.

Many research programs on non-model species biology have been empowered by genomics. In turn, genomics is underpinned by a reference sequence and ancillary information created by so-called \"genome projects\". The most reliable genome projects are the ones created as part of an active research program and designed to address specific questions but their life extends past publication. In this opinion paper I outline four key insights that have facilitated maintaining genomic communities: the key role of computational capability, the iterative process of building genomic resources, the value of community participation and the importance of manual curation. Taken together, these ideas can and do ensure the longevity of genome projects and the growing non-model species community can use them to focus a discussion with regards to its future genomic infrastructure.