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.
Enables users to work with high-throughput sequencing data. HTSeq is a program that simplifies development of scripts for processing and analyzing high-throughput sequencing (HTS) data. It contains parsers for common file formats for a variety of types of input data and is suitable as a general platform for a diverse range of tasks.
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.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Provides a collection of mathematical algorithms and convenience functions built on the Numpy extension of Python. SciPy consists of an ecosystem offering open source software for scientific computing in Python. Users can utilize commands and classes for manipulating and visualizing data. This program is organized into subpackages covering different scientific computing domains. It can be useful for mathematics, science, and engineering.
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.
Aims to be a collection of small sequence processing utilities. seq_crumbs is modeled after the Unix command line text processing utilities so every utility tries to perform a specific task and most of them take a sequence file as input and create a new processed sequence file as output. This design encourages the assembly of the seq_crumbs utilities with Unix pipes to create complex pipelines.
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.