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Open Chemistry Project: BEDtools "Genome arithmetic"—manipulation of coordinate sets and the extraction of sequences from a BED file. Linux: MIT: QuinlanLab, University of Utah: Bioclipse: Visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP) Linux, macOS, Windows [1] Eclipse Public: The Bioclipse ...
List of open-source bioinformatics software; Alternatively, here is a categorization according to the respective bioinformatics subfield specialized on: Sequence analysis software. List of sequence alignment software; List of alignment visualization software; Alignment-free sequence analysis; De novo sequence assemblers; List of gene prediction ...
This server includes many bioinformatics tools that are widely useful in many areas of genomics research. Users can create logins, and save histories, workflows, and datasets on the server. These saved items can also be shared with others. As open-source software that can be downloaded, installed and customized to address specific needs. [20]
Open-source, written in pure Java; supports all platforms with no recompilation and no other dependencies. ContextMap was developed to overcome some limitations of other mapping approaches, such as resolution of ambiguities. The central idea of this tool is to consider reads in gene expression context, improving this way alignment accuracy.
Parabricks offers workflows for DNA and RNA analyses and the detection of germline and somatic mutations, using open-source tools. [1] It is designed to improve the computing time of genomic data analysis while maintaining the flexibility required for various bioinformatics experiments. [1]
Performs affine-transform-optimized global alignment, which is slower but more accurate than Smith-Waterman. Handles Illumina, 454, PacBio, Sanger, and Ion Torrent data. Splice-aware; capable of processing long indels and RNA-seq. Pure Java; runs on any platform. Used by the Joint Genome Institute. Yes Yes Yes Yes Free, BSD: 2010 BFAST
geWorkbench [2] (genomics Workbench) is an open-source software platform for integrated genomic data analysis. It is a desktop application written in the programming language Java. geWorkbench uses a component architecture.
Nextflow comes with specific executors for various platforms, including major cloud providers. It supports the following environments for pipeline execution: [ 16 ] Local : This is the default executor where Nextflow pipelines run on Linux or Mac OS, and the execution occurs on the computer where the pipeline is launched.