Twelve years of SAMtools and BCFtools

Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. Findings The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Conclusion Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.

The Popgen Pipeline Platform: A Software Platform for Facilitating Population Genomic Analyses

Here we present the Pop-Gen Pipeline Platform (PPP), a software platform with the goal of reducing the computational expertise required for conducting population genomic analyses. The PPP was designed as a collection of scripts that facilitate common population genomic workflows in a consistent and standardized Python environment. Functions were developed to encompass entire workflows, including: input preparation, file format conversion, various population genomic analyses, output generation, and visualization. By facilitating entire workflows, the PPP offers several benefits to prospective end users - it reduces the need of redundant in-house software and scripts that would require development time and may be error-prone, or incorrect. The platform has also been developed with reproducibility and extensibility of analyses in mind. The PPP is an open-source package that is available for download and use at https://ppp.readthedocs.io/en/latest/PPP_pages/install.html

CAD/CAM of Clothing Laser Cutting

The paper takes computer digital image processing as a foundation, laboratory analysis as the confirmation method, and takes garment industry production as the application production, researching the information characteristic of the clothing image design, the signal extraction, and the basic conversion rule in order to explore the computer-aided design of clothing pattern, apparel images (CAD), as well as the achievement of automatic laser cutting on complex design and apparel-hanging through the information technology. The topic emphatically discusses different graphic file format conversion technology and establishes the best craft parameter database that suits the laser cutting via the ACCESS software, while carrying on the shape error and precision analysis. The topic research conclusion will provide effective, reliable technology and the data support for the laser cutting craft in fashion industry. And it will enhance the laser processing efficiency of the fashion and the apparel hanging as well as guarantee the cutting quality to achieve the best effect.

CURVIS: a program to study and analyse crystallographic structures and phase transitions

The visualization of scientific data is, nowadays, of extreme importance. Phase transitions, the topology of a crystallographic system, the electron density distribution inside a lattice or the changes in crystal structure during phase transitions cannot be fully investigated without the help of proper visualization. The programCURVIS(downloadable free of charge upon request) was developed as a tool for investigating crystal structures and occurring transitions. In this tool, some features are implemented to analyse, display and manage the three-dimensional structure of crystals and single molecules. More importantly,CURVIScan generate and handle hyperbolic surfaces in three dimensions, and provide specific routines to perform calculations of curvature and energy of such surfaces. The most important features are (i) file format conversion (with assignment of the atom types and atomic charges), (ii) surface calculation and (iii) curvature and surface-energy analysis.