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BAMBUS: A hierarchical approach to building contig scaffolds |
Overview
BAMBUS is the first publicly available
scaffolding program. It orders and orients contigs into scaffolds based
on various types of linking information. Additionally, BAMBUS allows
the users to build scaffolds in a hierarchical fashion by prioritizing
the order in which links are used. For more information please check
out the online documentation.
Note
that currently Bambus is undergoing a transition in order to be
integrated with the AMOS package. Please stay tuned for a new and
improved release!
System requirements
Bambus is released as source code and was tested on Linux RedHat 6.x+, Sun Solaris, and Alpha OSF1, but should work on any Unix system. Additionally your system must have at least Perl 5.6 and the XML::Parser and Config::IniFiles modules installed. The dot program from the AT&T Graphviz package must be installed on your system in order to generate Postscript images of scaffolds.
Obtaining BAMBUS
This software is OSI Certified
Open Source Software.
The Bambus source if freely available for download from the File Release Section of our SourceForge project page.
To receive information regarding new releases and developments, please subscribe to our moderated, low-traffic users' mailing list:
Documentation
The distribution includes detailed documentation of all the file formats used. Additionally, a basic user manual is available here.
Data
In addition to the simple test data provided in the source package you can download a more complex example from: ftp://ftp.bcb.umd.edu/pub/data/assembly/bambus-data.tar.gz.
Contact Information
For Bambus bug reports, support requests, or any other inquiries please browse our SourceForge project page or Email us at:
References
M. Pop, D. Kosack, S. L. Salzberg. A hierarchical approach to building contig scaffolds. Genome Research 14(1), pp. 149-159, 2004.