BFAST 0.7.0a has been released.
In this version, there is new support for paired end and mate pair data. Gone is the inefficient paired end rescue mode that never really worked. Replacing this is a new pairing step (no rescue) that more intelligently chooses pairs of alignments. Use the "-Y" option, or the "-S" or "-P" options if you have oddly paired reads, to indicate the type of pairing in your library.
Also, a new mapping quality calculation is included (tired of those old 255 mapqs?). These mapping qualities are better calibrated, and will improve downstream variant calling.
For SOLiD reads, choose how base qualities are calculated from color qualities using the "-b" option. This can reduce false positives at the cost of sensitivity, especially for tools that use base qualities in their SNP calling models.
Of course, bfast+bwa has also been updated, so all the new features are included there.
Many thanks to the users and contributors! As always, please send comments, suggestions, bugs, and associated fixes to email@example.com,