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 easyfm: An easy software suite for file manipulation of Next Generation Sequencing data on desktops

2021 ◽  
Author(s):  
Hyungtaek Jung ◽  
Brendan Jeon ◽  
Daniel Ortiz-Barrientos
Keyword(s):  
Next Generation Sequencing ◽  
Life Sciences ◽  
Next Generation Sequencing Data ◽  
Command Line ◽  
Next Generation ◽  
Web Based ◽  
File Formats ◽  
Wide Range ◽  
Ngs Data ◽  
Generation Sequencing

Storing and manipulating Next Generation Sequencing (NGS) file formats for understanding biological phenomena is an essential but difficult task in the life sciences. Yet, most methods for analysing NGS data require complex command-line tools in high-performance computing (HPC) or web-based servers and have not yet been implemented in comprehensive, easy-to-use software. Here we present easyfm (easy file manipulation), a free standalone Graphical User Interface (GUI) software with Python support that can be used to facilitate the rapid discovery of target sequences (or user’s interest) in NGS datasets for novice users (more accessible to biologists). It enables them to perform end-to-end reproducible data analyses using a desktop application (Windows, Mac and Linux). Unlike existing tools, the GUI-based easyfm is not dependent on any HPC system and can be operated without an internet connection. For user-friendliness and convenience, easyfm was developed with four work modules and a secondary GUI window, covering different aspects of NGS data analysis, including post-processing, filtering, format conversion, generating results, real-time log, and help. In combination with the executable tools (BLAST+ and BLAT) and Python, easyfm allows the user to set analysis parameters, select/extract regions of interest, examine the input and output results, and convert to a wide range of file formats. To help augment the functionality of existing web-based and command-line tools, easyfm, a self-contained program, comes with extensive documentation (https://github.com/TaekAndBrendan/easyfm). This specific benefit allows easyfm to seamlessly integrate visual and interactive representations of NGS files, supporting a wider scope of bioinformatics applications in the life sciences.

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