Bambus

Overview

Bambus is the first general purpose scaffolder that is publicly available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

Publication: "Hierarchical scaffolding with Bambus." Pop M, Kosack DS, Salzberg SL, Genome Research, 2004. 14(1):149-59.

Note: Bambus is undergoing a transition in order to be integrated with the AMOS package. Please stay tuned for a new and improved release!

Documentation

The distribution includes detailed documentation of all the file formats used. Additionally, a basic user manual is available here.

In addition to the simple test data provided in the source package you can download a more complex example from: ftp://ftp.cbcb.umd.edu/pub/data/assembly/bambus-data.tar.gz.

Acknowledgements

The development of BAMBUS was supported by the National Science Foundation under grant KDI-9980088.