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Bamformatics

The Bamformatics project aims to play two distinct roles. First, it provides a coherent toolkit for analysis of high-throughput sequencing data in post-alignment stages. Second, the project also implements a graphical user interface to facilitate use of the toolkit as well as execution of general pipelines and workflows.

Toolkit

The constituents of the Bamformatics toolkit can be split into the following groups:

• [Variants] – tools associated with variant calling and filtering,
• [Tracks] – tools associated with genomic tracks derived from alignments,
• [Other] – miscellaneous tools, e.g. statistics.

Some of the functionality described in the above pages overlaps with that of other programs (see [Resources]). However, the Bamformatics toolkit has a number of interesting and distinguishing [Features].

GUI

The graphical user interface is designed as a file-manager. This should make its general look-and-feel familiar and at the same time provide access to advanced features. Its functionality is described under the following headings:

• [GUI] – general information about the GUI,
• [GUIvariants] – access to the toolkit's programs related to variant calling and filtering,
• [GUIscripts] – handling of generic scripts and complete pipelines.

Note: The GUI is an experimental component of the project.

Resources

Some additional relevant information

• [Resources] – links to related and/or complementary software of HTS data analysis,
• [Libraries] – third-party libraries and components used within this project,
• [Versions] – history of updates.

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Please send comments or bug reports to 'bamformatics at gmail dot com'.