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Libraries/Frameworks | High-throughput sequencing data analysis

High throughput sequencing (HTS) has become one of the primary experimental tools used to extract genomic information from biological samples. Bioinformatics tools are continuously being developed for the analysis of HTS data. Beyond some well-defined core analyses, such as quality control or genomic alignment, the consistent development of custom tools and the representation of sequencing data in organized computational structures and entities remains a challenging effort for bioinformaticians. Maragkakis et al., 2015.

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Biopython
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Provides a set of tools for biological computation written in Python. Biopython contains modules for reading and writing different sequence files formats and multiple sequence alignments, interacting with common tools (such as BLAST, ClustalW and EMBOSS), accessing key online databases, handling with 3D macro molecular structures and furnishing numerical methods for statistical learning. The main goal of this platform is to facilitate the use of Python for bioinformatics by generating reusable modules and classes.
BioPerl
Manages and manipulates life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. It is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists. It provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project.
BioJS
An open-source project whose main objective is the visualization of biological data in JavaScript. BioJS provides an easy-to-use consistent framework for bioinformatics application programmers. It follows a community-driven standard specification that includes a collection of components purposely designed to require a very simple configuration and installation. In addition to the programming framework, BioJS provides a centralized repository of components available for reutilization by the bioinformatics community.
PILGRM / Platform for Interactive Learning by Genomics Results Mining
Generates specific biological hypotheses by directing the supervised analyses of global microarray expression collections. PILGRM is a platform for interactive learning by genomics results mining. It brings sophisticated machine learning methods applied to enormous gene expression compendia into the lab of any researcher, enabling data driven experiment direction complementary to traditional knowledge-based discovery provided by existing databases.
CracTools
Integrated pipelines for RNA-Seq analysis using CRAC (mapping tool) additional fields. CracTools are a complete toolbox designed to build pipelines on top of CRAC. CracTools are based on the “CracTools-core”, the key modules allowing to: (i) Extract CRAC information using specific data structures, (ii) Extract BAM lines, BED lines and such using dedicated intervaltree structures, (iii) Provide simply tools to extract CRAC features, combine different files, and count reads inside a region.
BioRuby
Contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser.
Biospark
Provides a platform dedicated to storage and analysis of large binary numerical datasets using Hadoop and Spark. Biospark supplies abstractions for parallel analysis of standard data types such as multidimensional arrays and images. The application also includes modules of file conversion to ease the parallel analysis of specific datasets, including molecular dynamics simulations or time-lapse microscopy. In addition, it contains reference implementations of several commonly-used analysis.
Bpipe
Allows definition and execution of bioinformatics pipelines. Bpipe was created in response to a need to frequently run many variations of a pipeline with stages deleted, inserted, reordered or adjusted. The software is implemented in, a language that supports creation of Domain-Specific Languages for the Java Virtual Machine, and it does not require knowledge of either language to implement pipelines. It includes features such as automatic connection of stages, audit trail or transactional management of tasks.
Omics Pipe
A computational framework that automates multi-omics data analysis pipelines on high performance compute clusters and in the cloud. It supports best practice published pipelines for RNA-seq, miRNA-seq, Exome-seq, Whole Genome sequencing, ChIP-seq analyses and automatic processing of data from The Cancer Genome Atlas (TCGA). Omics Pipe provides researchers with a tool for reproducible, open source and extensible next generation sequencing analysis. The goal of Omics Pipe is to democratize NGS analysis by dramatically increasing the accessibility and reproducibility of best practice computational pipelines, which will enable researchers to generate biologically meaningful and interpretable results.
BioQueue
Improves the efficiency and robustness of bioinformatics research. BioQueue provides a web-based workbench and implements an explicit syntax to keep an optimal balance between flexibility and simplicity. This resource implements a greedy algorithm to dispatch jobs with these estimated data to achieve an optimal balance between the efficiency and system resources (CPU, memory and disk). User can export a protocol with a generated model as a plain text file, and then upload the protocol to any forum or our open platform
Bio-Docklets
Aims to perform basic analysis and interpretation of datasets with minimal effort. Bio-Docklets is an approach for abstracting the complex data operations of multi-step, bioinformatics pipelines for Next Generation Sequencing (NGS) data analysis. It also run a large number of pipeline instances for concurrent analysis of multiple datasets. It enables easy access to NGS data analysis pipelines for non-bioinformatics experts, on any computing environment whether a laboratory workstation, university computer cluster, or a cloud service provider.
SUSHI / Support Users for SHell-script Integration
An agile data analysis framework that relieves bioinformaticians from the administrative challenges of their data analysis. SUSHI lets users build reproducible data analysis workflows from individual applications and manages the input data, the parameters, meta-information with user-driven semantics, and the job scripts. As distinguishing features, SUSHI provides an expert command line interface as well as a convenient web interface to run bioinformatics tools. SUSHI datasets are self-contained and self-documented on the file system. This makes them fully reproducible and ready to be shared. With the associated meta-information being formatted as plain text tables, the datasets can be readily further analyzed and interpreted outside SUSHI.
Butler
Enables scientific analysis on multiple cloud platforms. Butler includes four sub-systems which provide a way for (i) create and tears down clusters on several clouds, including defining Virtual Machines (VMs), or storage (ii) install and configure software on virtual machines, (iii) allow users to define and run scientific workflows on the cloud, and (iv) be a set of tools for ensuring continuous successful operation of the virtualized environment, as well as for troubleshooting error conditions.
GenomeTools
Follows the annotation graph approach, offering a unified graph-based representation. GenomeTools is a software library and an associated software tools for developing bioinformatics software intended to create, process or convert annotation graphs. To process large annotation sets with low memory overhead, the tool has been designed and implemented as an pull-based approach for sequential processing of annotations. This allows to handle even the largest annotation sets, such as a complete catalogue of human variations.
Fastr
Creates and manages processing pipelines. Fastr is an image processing workflow framework that speeds up the development cycle for creating workflows and minimizes the introduction of errors. The software is designed to build workflows that are agnostic to where (i) the input data are stored, (ii) the resulting output data should be stored, (iii) the steps in the workflow will be executed, and (iv) what information about the data and processing needs to be logged for data provenance.
Rbbt / Ruby Bioinformatics Toolkit
A framework for software development in bioinformatics. Rbbt covers three aspects: 1) Developing functionalities, 2) making them as widely accessible as possible and 3) integrating them with one another. It was intended initially to hold different low level tools that for the basis of most bioinformatics work: parsing and tidying data, gathering resources, organizing the sequential production of results for reusable/reproducible work. The framework provides incentives to adhere to several reasonable standards that improve reusability and interoperability and has thus resulted in a very comprehensive set of functionalities that now form one of the most ambitions bioinformatics frameworks available.
EBiAn / Easy Bioinformatics Analysis
Performs the main analysis and manipulation of DNA, RNA, proteins and peptides sequences. EBiAn offers tools to enable the more routinely analysis used in preliminary computational approaches to experimental laboratory practices in the biochemistry and molecular biology area. The package includes (i) format conversions tools like GenBank to Fasta, EMBL to Fasta, ToThreeLetterCode and ToOneLetterCode, (ii) DNA tools like DNA/RNA-Param, DNA Cutter and many others, (iii) peptides and proteins tools like MS-Digest, PepBuilder and many others.
LATITUDES Network / Library of Assessment Tools and InsTruments Used to assess Data validity in Evidence Syntheses
Improves the process of quality assessment in systematic reviews. LATITUDES Network allows the development of quality assessment tools. It provides different tools for: (1) diagnostic accuracy studies; (2) systematic reviews; (3) prediction modelling studies; and (4) non-randomised studies of interventions and the new version of the Cochrane risk of bias tool for randomised trials. This tool aims to highlight and increase the use of key risk of bias assessment tools.
GenOO
An open-source, object-oriented (OO) Perl framework specifically developed for the design and implementation of HTS analysis tools. GenOO models biological entities such as genes and transcripts as Perl objects, and includes relevant modules, attributes and methods that allow for the manipulation of high throughput sequencing data. GenOO integrates these elements in a simple and transparent way which allows for the creation of complex analysis pipelines minimizing the overhead for the researcher. Using GenOO as a core development module can greatly benefit users, by reducing the overhead and complexity of managing HTS data and biological entities at hand.
blend4php
Offers a partial implementation of the Galaxy API and includes support for datasets, data types, folder contents, folders, genomes, group roles, groups, group users, histories, history contents, jobs, libraries, library contents, requests, roles, search, tools, toolshed repositories, users, visualizations and workflows. Blend4php package is a PHP wrapper for the Galaxy Application Programming Interface (API). Blend4php library wraps Galaxy's RESTful API into a PHP-based library. PHP-based web applications can use blend4php to automate execution, monitoring and management of a remote Galaxy server, including its users, workflows, jobs and more.
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