scholarly journals ASaiM: a Galaxy-based framework to analyze raw shotgun data from microbiota

2017 ◽  
Author(s):  
Bérénice Batut ◽  
Kévin Gravouil ◽  
Clémence Defois ◽  
Saskia Hiltemann ◽  
Jean-François Brugère ◽  
...  
Keyword(s):  
Technological Progress ◽  
Source Code ◽  
Command Line ◽  
Bioinformatic Tools ◽  
Link Type ◽  
Data Analyses ◽  
The Galaxy ◽  
Sequencing Platforms ◽  
User Friendly ◽  
New Generation

AbstractBackgroundNew generation of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies.FindingsWe therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides a curated collection of tools to explore and visualize taxonomic and functional information from raw amplicon, metagenomic or metatranscriptomic sequences. To guide different analyses, several customizable workflows are included. All workflows are supported by tutorials and Galaxy interactive tours to guide the users through the analyses step by step. ASaiM is implemented as Galaxy Docker flavour. It is scalable to many thousand datasets, but also can be used a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io/)ConclusionsBased on the Galaxy framework, ASaiM offers sophisticated analyses to scientists without command-line knowledge. ASaiM provides a powerful framework to easily and quickly explore microbiota data in a reproducible and transparent environment.

scholarly journals idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates

2020 ◽  
Author(s):  
Xun Zhu ◽  
Ti-Cheng Chang ◽  
Richard Webby ◽  
Gang Wu
Keyword(s):  
Personal Computer ◽  
Source Code ◽  
Command Line ◽  
Sequencing Data ◽  
Link Type ◽  
Public Dataset ◽  
Virus Isolates

AbstractidCOV is a phylogenetic pipeline for quickly identifying the clades of SARS-CoV-2 virus isolates from raw sequencing data based on a selected clade-defining marker list. Using a public dataset, we show that idCOV can make equivalent calls as annotated by Nextstrain.org on all three common clade systems using user uploaded FastQ files directly. Web and equivalent command-line interfaces are available. It can be deployed on any Linux environment, including personal computer, HPC and the cloud. The source code is available at https://github.com/xz-stjude/idcov. A documentation for installation can be found at https://github.com/xz-stjude/idcov/blob/master/README.md.

scholarly journals DamageProfiler: Fast damage pattern calculation for ancient DNA

2021 ◽  
Author(s):  
Judith Neukamm ◽  
Alexander Peltzer ◽  
Kay Nieselt
Keyword(s):  
Ancient Dna ◽  
Source Code ◽  
Supplementary Information ◽  
Command Line ◽  
Central Importance ◽  
Command Line Interface ◽  
Analysis Pipeline ◽  
File Formats ◽  
Programming Knowledge ◽  
User Friendly

Abstract Motivation In ancient DNA research, the authentication of ancient samples based on specific features remains a crucial step in data analysis. Because of this central importance, researchers lacking deeper programming knowledge should be able to run a basic damage authentication analysis. Such software should be user-friendly and easy to integrate into an analysis pipeline. Results DamageProfiler is a Java based, stand-alone software to determine damage patterns in ancient DNA. The results are provided in various file formats and plots for further processing. DamageProfiler has an intuitive graphical as well as command line interface that allows the tool to be easily embedded into an analysis pipeline. Availability All of the source code is freely available on GitHub (https://github.com/Integrative-Transcriptomics/DamageProfiler). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Phigaro: high throughput prophage sequence annotation

2019 ◽  
Author(s):  
Elizaveta V. Starikova ◽  
Polina O. Tikhonova ◽  
Nikita A. Prianichnikov ◽  
Chris M. Rands ◽  
Evgeny M. Zdobnov ◽  
...  
Keyword(s):  
Test Data ◽  
High Throughput ◽  
Source Code ◽  
Sequence Annotation ◽  
Command Line ◽  
Link Type ◽  
Genome Maps ◽  
Transposon Insertion ◽  
Prophage Sequence

AbstractSummaryPhigaro is a standalone command-line application that is able to detect prophage regions taking raw genome and metagenome assemblies as an input. It also produces dynamic annotated “prophage genome maps” and marks possible transposon insertion spots inside prophages. It provides putative taxonomic annotations that can distinguish tailed from non-tailed phages. It is applicable for mining prophage regions from large metagenomic datasets.AvailabilitySource code for Phigaro is freely available for download at https://github.com/bobeobibo/phigaro along with test data. The code is written in Python.

scholarly journals re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11333
Author(s):  
Daniyar Karabayev ◽  
Askhat Molkenov ◽  
Kaiyrgali Yerulanuly ◽  
Ilyas Kabimoldayev ◽  
Asset Daniyarov ◽  
...  
Keyword(s):  
Web Application ◽  
High Throughput Sequencing ◽  
Sequencing Data ◽  
Data Types ◽  
Standard Format ◽  
Standard Data ◽  
Additional Information ◽  
Link Type ◽  
Sequencing Platforms ◽  
User Friendly

Background High-throughput sequencing platforms generate a massive amount of high-dimensional genomic datasets that are available for analysis. Modern and user-friendly bioinformatics tools for analysis and interpretation of genomics data becomes essential during the analysis of sequencing data. Different standard data types and file formats have been developed to store and analyze sequence and genomics data. Variant Call Format (VCF) is the most widespread genomics file type and standard format containing genomic information and variants of sequenced samples. Results Existing tools for processing VCF files don’t usually have an intuitive graphical interface, but instead have just a command-line interface that may be challenging to use for the broader biomedical community interested in genomics data analysis. re-Searcher solves this problem by pre-processing VCF files by chunks to not load RAM of computer. The tool can be used as standalone user-friendly multiplatform GUI application as well as web application (https://nla-lbsb.nu.edu.kz). The software including source code as well as tested VCF files and additional information are publicly available on the GitHub repository (https://github.com/LabBandSB/re-Searcher).

scholarly journals HaVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences

2021 ◽  
Author(s):  
Phuoc Truong Nguyen ◽  
Ilya Plyusnin ◽  
Tarja Sironen ◽  
Olli Vapalahti ◽  
Ravi Kant ◽  
...  
Keyword(s):  
South African ◽  
Genetic Variance ◽  
Source Code ◽  
Bioinformatic Pipeline ◽  
Related Research ◽  
Bioinformatic Tools ◽  
Link Type ◽  
Novel Variants ◽  
The Uk ◽  
Virus Genomes

AbstractBackgroundSARS-CoV-2 related research has increased in importance worldwide since December 2019. Several new variants of SARS-CoV-2 have emerged globally, of which the most notable and concerning currently are the UK variant B.1.1.7, the South African variant B1.351 and the Brazilian variant P.1. Detecting and monitoring novel variants is essential in SARS-CoV-2 surveillance. While there are several tools for assembling virus genomes and performing lineage analyses to investigate SARS-CoV-2, each is limited to performing singular or a few functions separately.ResultsDue to the lack of publicly available pipelines, which could perform fast reference-based assemblies on raw SARS-CoV-2 sequences in addition to identifying lineages to detect variants of concern, we have developed an open source bioinformatic pipeline called HaVoC (Helsinki university Analyzer for Variants Of Concern). HaVoC can reference assemble raw sequence reads and assign the corresponding lineages to SARS-CoV-2 sequences.ConclusionsHaVoC is a pipeline utilizing several bioinformatic tools to perform multiple necessary analyses for investigating genetic variance among SARS-CoV-2 samples. The pipeline is particularly useful for those who need a more accessible and fast tool to detect and monitor the spread of SARS-CoV-2 variants of concern during local outbreaks. HaVoC is currently being used in Finland for monitoring the spread of SARS-CoV-2 variants. HaVoC user manual and source code are available at https://www.helsinki.fi/en/projects/havoc and https://bitbucket.org/auto_cov_pipeline/havoc, respectively.

scholarly journals SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts

2020 ◽  
Author(s):  
R. Zhang ◽  
M. Mirdita ◽  
E. Levy Karin ◽  
C. Norroy ◽  
C. Galiez ◽  
...  
Keyword(s):  
Open Source ◽  
Protein Level ◽  
De Novo ◽  
False Positives ◽  
Metagenomic Data ◽  
Command Line ◽  
Link Type ◽  
Host Relationships ◽  
User Friendly

SummarySpacePHARER (CRISPR Spacer Phage-Host Pair Finder) is a sensitive and fast tool for de novo prediction of phage-host relationships via identifying phage genomes that match CRISPR spacers in genomic or metagenomic data. SpacePHARER gains sensitivity by comparing spacers and phages at the protein-level, optimizing its scores for matching very short sequences, and combining evidences from multiple matches, while controlling for false positives. We demonstrate SpacePHARER by searching a comprehensive spacer list against all complete phage genomes.Availability and implementationSpacePHARER is available as an open-source (GPLv3), user-friendly command-line software for Linux and macOS at spacepharer.soedinglab.org.

scholarly journals NanoPack: visualizing and processing long read sequencing data

2017 ◽  
Author(s):  
Wouter De Coster ◽  
Svenn D’Hert ◽  
Darrin T. Schultz ◽  
Marc Cruts ◽  
Christine Van Broeckhoven
Keyword(s):  
Web Service ◽  
Graphical User Interface ◽  
Source Code ◽  
Supplementary Information ◽  
Command Line ◽  
Sequencing Data ◽  
Link Type ◽  
Oxford Nanopore ◽  
Long Read ◽  
Oxford Nanopore Technologies

AbstractSummary: Here we describe NanoPack, a set of tools developed for visualization and processing of long read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences.Availability and Implementation: The NanoPack tools are written in Python3 and released under the GNU GPL3.0 Licence. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools.Contact:[email protected] information: Supplementary tables and figures are available at Bioinformatics online.

scholarly journals cblaster: a remote search tool for rapid identification and visualisation of homologous gene clusters

2020 ◽  
Author(s):  
Cameron L.M. Gilchrist ◽  
Thomas J. Booth ◽  
Yit-Heng Chooi
Keyword(s):  
Source Code ◽  
Gene Clusters ◽  
Rapid Identification ◽  
Large Datasets ◽  
Homologous Gene ◽  
Command Line ◽  
Local Sequence ◽  
Search Tool ◽  
User Friendly ◽  
Friendly Graphical User Interface

AbstractGenes involved in coordinated biological pathways, including metabolism, drug resistance and virulence, are often collocalised as gene clusters. Identifying homologous gene clusters aids in the study of their function and evolution, however existing tools are limited to searching local sequence databases. Tools for remotely searching public databases are necessary to keep pace with the rapid growth of online genomic data. Here, we present cblaster, a Python based tool to rapidly detect collocated genes in local and remote databases. cblaster is easy to use, offering both a command line and a user-friendly graphical user interface (GUI). It generates outputs that enable intuitive visualisations of large datasets, and can be readily incorporated into larger bioinformatic pipelines. cblaster is a significant update to the comparative genomics toolbox. cblaster source code and documentation is freely available from GitHub under the MIT license (github.com/gamcil/cblaster).

scholarly journals Galactic Circos: User-friendly Circos plots within the Galaxy platform

GigaScience ◽  
2020 ◽  
Vol 9 (6) ◽  
Author(s):  
Helena Rasche ◽  
Saskia Hiltemann
Keyword(s):  
Analytical Data ◽  
Genomic Analysis ◽  
Scientific Data ◽  
Ease Of Use ◽  
Command Line ◽  
Web Browser ◽  
The Galaxy ◽  
Unix Command ◽  
User Friendly ◽  
High Degree

Abstract Background Circos is a popular, highly flexible software package for the circular visualization of complex datasets. While especially popular in the field of genomic analysis, Circos enables interactive graphing of any analytical data, including alternative scientific domain data and non-scientific data. This high degree of flexibility also comes with a high degree of complexity, which may present an obstacle for researchers not trained in programming or the UNIX command line. The Galaxy platform provides a user-friendly browser-based graphical interface incorporating a broad range of “wrapped” command line tools to facilitate accessibility. Findings We have developed a Galaxy wrapper for Circos, thus combining the power of Circos with the accessibility and ease of use of the Galaxy platform. The combination substantially simplifies the specification and configuration of Circos plots for end users while retaining the power to produce publication-quality visualizations of complex multidimensional datasets. Conclusions Galactic Circos enables the creation of publication-ready Circos plots using only a web browser, via the Galaxy platform. Users may download the full set of Circos configuration files of their plots for further manual customization. This version of Circos is available as an open-source installable application from the Galaxy ToolShed, with its use clarified in a training manual hosted by the Galaxy Training Network.

scholarly journals Development of graphical user interface for open source VLSI digital synthesis tool Qflow

2018 ◽  
Vol 7 (2) ◽  
pp. 710
Author(s):  
K. Sripath Roy ◽  
K. Abhiram ◽  
M. Arun Sumanth ◽  
Jaishree Jaishankar ◽  
P. Abhishek ◽  
...  
Keyword(s):  
User Interface ◽  
Open Source ◽  
Graphical User Interface ◽  
Source Code ◽  
Command Line ◽  
Simulation Process ◽  
Vlsi Technology ◽  
Synthesis Tool ◽  
Digital Synthesis ◽  
User Friendly

There are many tools that are used for simulation in the domain of VLSI technology but none of them are easily accessible. There is a need for Free and open source tools in this stream so as to make them accessible to everyone. There are efficient tools that already exist in open source in VLSI stream but are not used widely because of their command line user interface. Hence, creating a user friendly interface will help many developers and users to work easily. This paper deals with the idea to solve the above issue by creating a Graphical User Interface for the open source VLSI tool called QFlow. Qflow is a tool used in synthesizing a VLSI circuit from the Verilog source code. There are multiple tools integrated with this tool to assure the simulation process. It is a combination of many dependencies that are used for synthesis, placement, layout viewing and routing in a fabrication process. All the independent tools used for the Verilog code simulation are integrated onto a single platform. Qt is used for creating the cross-stage application.

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