scholarly journals Bacting: a next generation, command line version of Bioclipse

2021 ◽  
Vol 6 (62) ◽  
pp. 2558
Author(s):  
Egon Willighagen
Keyword(s):  
Command Line ◽  
Next Generation ◽  
Command Line Version

Fortran90 sources of the subroutines ofUMWEG. III. TheUMWEG-specific subroutines

2007 ◽  
Vol 40 (1) ◽  
pp. 185-187
Author(s):  
Elisabeth Rossmanith
Keyword(s):  
Command Line ◽  
Main Program ◽  
Command Line Version

The Fortran90 sources of theUMWEG-specific subroutines of the programUMWEGare presented and deposited, together with the PostScript-plot software subroutines and the simple and short main program of the command-line version of the programUMWEG.

scholarly journals The UCSC Genome Browser database: 2018 update

2017 ◽  
Vol 46 (D1) ◽  
pp. D762-D769 ◽  
Author(s):  
Jonathan Casper ◽  
Ann S Zweig ◽  
Chris Villarreal ◽  
Cath Tyner ◽  
Matthew L Speir ◽  
...  
Keyword(s):  
Ucsc Genome Browser ◽  
Genome Browser ◽  
Gene Interactions ◽  
Command Line ◽  
Web Interface ◽  
Variant Annotation ◽  
The Past ◽  
Ucsc Genome Browser Database ◽  
Genome Assemblies ◽  
Command Line Version

Abstract The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis—12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences and an interactive navigator for gene interactions. Other upgrades from the past year include a command-line version of the Variant Annotation Integrator, support for Human Genome Variation Society variant nomenclature input and output, and a revised highlighting tool that now supports multiple simultaneous regions and colors.

scholarly journals The VEGA suite of programs: an versatile platform for cheminformatics and drug design projects

2020 ◽  
Author(s):  
Alessandro Pedretti ◽  
Angelica Mazzolari ◽  
Silvia Gervasoni ◽  
Laura Fumagalli ◽  
Giulio Vistoli
Keyword(s):  
Drug Design ◽  
Computational Chemistry ◽  
Source Code ◽  
Command Line ◽  
Design Studies ◽  
Non Profit ◽  
Flexible Architecture ◽  
Design Projects ◽  
Technology Level ◽  
Command Line Version

Abstract The purpose of the article is to offer an overview of the latest release of the VEGA suite of programs. This software has been constantly developed and freely released during the last 20 years and has now reached a significant diffusion and technology level as confirmed by the about 22 500 registered users. While being primarily developed for drug design studies, the VEGA package includes cheminformatics and modeling features, which can be fruitfully utilized in various contexts of the computational chemistry. To offer a glimpse of the remarkable potentials of the software, some examples of the implemented features in the cheminformatics field and for structure-based studies are discussed. Finally, the flexible architecture of the VEGA program which can be expanded and customized by plug-in technology or scripting languages will be described focusing attention on the HyperDrive library including highly optimized functions. Availability and implementation: The VEGA suite of programs and the source code of the VEGA command-line version are available free of charge for non-profit organizations at http://www.vegazz.net. Contact: [email protected]

scholarly journals pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 532 ◽  
Author(s):  
Saket Choudhary
Keyword(s):  
Next Generation Sequencing ◽  
Research Community ◽  
Command Line ◽  
Next Generation ◽  
Multiple Use ◽  
Sequencing Data ◽  
Sequence Read Archive ◽  
Python Package ◽  
Generation Sequencing ◽  
Ncbi Sequence Read Archive

The NCBI Sequence Read Archive (SRA) is the primary archive of next-generation sequencing datasets. SRA makes metadata and raw sequencing data available to the research community to encourage reproducibility and to provide avenues for testing novel hypotheses on publicly available data. However, methods to programmatically access this data are limited. We introduce the Python package, pysradb, which provides a collection of command line methods to query and download metadata and data from SRA, utilizing the curated metadata database available through the SRAdb project. We demonstrate the utility of pysradb on multiple use cases for searching and downloading SRA datasets. It is available freely at https://github.com/saketkc/pysradb.

scholarly journals A Fun Introductory Command Line Lesson: Next Generation Sequencing Quality Analysis with Emoji!

CourseSource ◽  
2021 ◽  
Vol 8 ◽  
Author(s):  
Rachael M. St. Jacques ◽  
William M. Maza ◽  
Sabrina D. Robertson ◽  
Andrew Lonsdale ◽  
Caylin S. Murray ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Quality Analysis ◽  
Command Line ◽  
Next Generation ◽  
Sequencing Quality ◽  
Generation Sequencing

VEGAS2: Software for More Flexible Gene-Based Testing

2014 ◽  
Vol 18 (1) ◽  
pp. 86-91 ◽  
Author(s):  
Aniket Mishra ◽  
Stuart Macgregor
Keyword(s):  
Association Studies ◽  
Genome Wide Association Studies ◽  
Command Line ◽  
Single Nucleotide ◽  
Web Based ◽  
Reference Set ◽  
Genome Wide ◽  
User Friendly ◽  
Further Development ◽  
Command Line Version

Gene-based tests such as versatile gene-based association study (VEGAS) are commonly used following per-single nucleotide polymorphism (SNP) GWAS (genome-wide association studies) analysis. Two limitations of VEGAS were that the HapMap2 reference set was used to model the correlation between SNPs and only autosomal genes were considered. HapMap2 has now been superseded by the 1,000 Genomes reference set, and whereas early GWASs frequently ignored the X chromosome, it is now commonly included. Here we have developed VEGAS2, an extension that uses 1,000 Genomes data to model SNP correlations across the autosomes and chromosome X. VEGAS2 allows greater flexibility when defining gene boundaries. VEGAS2 offers both a user-friendly, web-based front end and a command line Linux version. The online version of VEGAS2 can be accessed through https://vegas2.qimrberghofer.edu.au/. The command line version can be downloaded from https://vegas2.qimrberghofer.edu.au/zVEGAS2offline.tgz. The command line version is developed in Perl, R and shell scripting languages; source code is available for further development.

scholarly journals An integrated strategy for target SSR genotyping with toleration of nucleotide variations in the SSRs and flanking regions

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yongxue Huo ◽  
Yikun Zhao ◽  
Liwen Xu ◽  
Hongmei Yi ◽  
Yunlong Zhang ◽  
...  
Keyword(s):  
High Throughput ◽  
Targeted Sequencing ◽  
Command Line ◽  
Single Nucleotide ◽  
Web Based ◽  
Integrated Strategy ◽  
Single Nucleotide Variations ◽  
Ssr Genotyping ◽  
Flanking Regions ◽  
Command Line Version

Abstract Background With the broad application of high-throughput sequencing and its reduced cost, simple sequence repeat (SSR) genotyping by sequencing (SSR-GBS) has been widely used for interpreting genetic data across different fields, including population genetic diversity and structure analysis, the construction of genetic maps, and the investigation of intraspecies relationships. The development of accurate and efficient typing strategies for SSR-GBS is urgently needed and several tools have been published. However, to date, no suitable accurate genotyping method can tolerate single nucleotide variations (SNVs) in SSRs and flanking regions. These SNVs may be caused by PCR and sequencing errors or SNPs among varieties, and they directly affect sequence alignment and genotyping accuracy. Results Here, we report a new integrated strategy named the accurate microsatellite genotyping tool based on targeted sequencing (AMGT-TS) and provide a user-friendly web-based platform and command-line version of AMGT-TS. To handle SNVs in the SSRs or flanking regions, we developed a broad matching algorithm (BMA) that can quickly and accurately achieve SSR typing for ultradeep coverage and high-throughput analysis of loci with SNVs compatibility and grouping of typed reads for further in-depth information mining. To evaluate this tool, we tested 21 randomly sampled loci in eight maize varieties, accompanied by experimental validation on actual and simulated sequencing data. Our evaluation showed that, compared to other tools, AMGT-TS presented extremely accurate typing results with single base resolution for both homozygous and heterozygous samples. Conclusion This integrated strategy can achieve accurate SSR genotyping based on targeted sequencing, and it can tolerate single nucleotide variations in the SSRs and flanking regions. This method can be readily applied to divergent sequencing platforms and species and has excellent application prospects in genetic and population biology research. The web-based platform and command-line version of AMGT-TS are available at https://amgt-ts.plantdna.site:8445 and https://github.com/plantdna/amgt-ts, respectively.

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