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+The short read alignment component (bwa-short) has been published:
+Li H. and Durbin R. (2009) Fast and accurate short read alignment
+with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60.
+
+If you use BWA-SW, please cite:
+Li H. and Durbin R. (2010) Fast and accurate long-read alignment with
+Burrows-Wheeler Transform. Bioinformatics, Epub.