SUMMARY: VISOR is a tool for haplotype-specific simulations of simple and complex structural variants (SVs). The method is applicable to haploid, diploid or higher ploidy simulations for bulk or single-cell sequencing data. SVs are implanted into FASTA haplotypes at single-basepair resolution, optionally with nearby single-nucleotide variants. Short or long reads are drawn at random from these haplotypes using standard error profiles. Double- or single-stranded data can be simulated and VISOR supports the generation of haplotype-tagged BAM files. The tool further includes methods to interactively visualize simulated variants in single-stranded data. The versatility of VISOR is unmet by comparable tools and it lays the foundation to simulate haplotype-resolved cancer heterogeneity data in bulk or at single-cell resolution. AVAILABILITY AND IMPLEMENTATION: VISOR is implemented in python 3.6, open-source and freely available at https://github.com/davidebolo1993/VISOR. Documentation is available at https://davidebolo1993.github.io/visordoc/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: The past few years have seen the emergence of nanopore-based sequencing technologies which interrogate single molecule of DNA and generate reads sequentially. RESULTS: In this paper, we demonstrate that, thanks to the sequentiality of the nanopore process, the data generated in the first tens of minutes of a typical MinION/GridION run can be exploited to resolve the alterations of a human genome at a karyotype level with a resolution in the order of tens of Mb, while the data produced in the first 6-12 h allow to obtain a resolution comparable to currently available array-based technologies, and thanks to a novel probabilistic approach are capable to predict the allelic fraction of genomic alteration with high accuracy. To exploit the unique characteristics of nanopore sequencing data we developed a novel software tool, Nano-GLADIATOR, that is capable to perform copy number variants/alterations detection and allelic fraction prediction during the sequencing run ('On-line' mode) and after experiment completion ('Off-line' mode). We tested Nano-GLADIATOR on publicly available ('Off-line' mode) and on novel whole genome sequencing dataset generated with MinION device ('On-line' mode) showing that our tool is capable to perform real-time copy number alterations detection obtaining good results with respect to other state-of-the-art tools. AVAILABILITY AND IMPLEMENTATION: Nano-GLADIATOR is freely available at https://sourceforge.net/projects/nanogladiator/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

We study the partially ordered set $P(a_1,\ldots, a_n)$ of all multidegrees $(b_1,\dots,b_n)$ of monomials $x_1^{b_1}\cdots x_n^{b_n}$, which properly divide $x_1^{a_1}\cdots x_n^{a_n}$. We prove that the order complex $\Delta(P(a_1,\dots,a_n))$ of $P(a_1,\ldots a_n)$ is (nonpure) shellable by showing that the order dual of $P(a_1,\ldots,a_n)$ is $CL$-shellable. Along the way, we exhibit the poset $P(4,4)$ as a new example of a poset with $CL$-shellable order dual that is not $CL$-shellable itself. For $n = 2$, we provide the rank of all homology groups of the order complex $\Delta ( P(a_1,a_2) )$. Furthermore, we give a succinct formula for the Euler characteristic of $\Delta ( P(a_1,a_2) )$.