Source code and Ubuntu 10.04 (64-bit) packages of iBWA Alpha v0.5 are now available for testing. iBWA is a fork of Heng Li's BWA aligner with support for iteratively adding alternate haplotypes, reference patches, and variant hypotheses. This enables you to leverage existing tools and pipelines in the diverse BWA ecosystem while also creating new analysis opportunities.

• Take advantage of improvements to the human reference made available by the Genome Reference Consortium.
• Represent alternate alignments in the context of the primary human reference.

For additional information about BWA please see Heng Li's BWA @ SourceForge or BWA's manual page.