Archaeopteryx

Archaeopteryx

Archaeopteryx is an open-source genome browser and annotation tool that allows users to visualize, manage, and analyze genomic datasets. It supports a range of common genomics file formats and provides features like dynamic zooming, metadata editing, and sharing sessions.
Science & Education Bioinformatics
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Archaeopteryx: Open-Source Genome Browser & Annotation Tool

An open-source genome browser and annotation tool for visualizing, managing, and analyzing genomic datasets with support for common genomics file formats and features like dynamic zooming and metadata editing.

What is Archaeopteryx?

Archaeopteryx is an open-source, Java-based genome browser and annotation visualization tool developed at the Broad Institute. It allows users to interactively explore genome assemblies and annotations, supporting a range of common genomics file formats including FASTA, GFF3, BED, WIG, and VCF.

Some key features of Archaeopteryx include:

  • Dynamic zooming and panning to navigate genome views
  • Custom track loading for visualizing datasets like alignments, variants, and gene models
  • Metadata editing such as adding comments and setting feature statuses
  • Session sharing and collaboration via saved sessions
  • Data integration from online databases like GenBank and UCSC
  • Programmatic access via CLI and APIs for advanced analysis and integration

Archaeopteryx aims to provide an intuitive yet powerful platform for genomicists, molecular biologists, and bioinformaticians to visualize, understand, and generate insights from genomic data. Its open-source availability also allows customization for specific research needs. Key use cases include exploring annotations of newly sequenced genomes, assessing variant calls, and integrating analyses into workflows and publications.

Archaeopteryx Features

Features

  1. Visualize genomic data
  2. Support for common file formats like FASTA, GenBank, GFF3
  3. Annotation editing
  4. Session sharing and collaboration
  5. Dynamic zooming and navigation
  6. Integrates with Galaxy for workflow management

Pricing

  • Open Source

Pros

Open source and free to use

Lightweight and easy to install

Active development community

Customizable and extensible via plugins

Cross-platform compatibility

Cons

Limited built-in analysis tools compared to desktop genome browsers

Less scalable for very large datasets

Steeper learning curve than some alternatives

Official Links

Official Website
https://sites.google.com/site/cmzmasek/home/sof...

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