Greetings all.

New versions of ChimeraSlayer, WigeoN, and NAST-iEr are released on sourceforge at:

http://sourceforge.net/projects/microbiomeutil/files/

Not much has changed with WigeoN or NAST-iEr other than small adjustments to be fully compatible with the latest set of trusted 16S reference sequences, available here:
http://sourceforge.net/projects/microbiomeutil/files/SequenceResources/SequenceResources_r11092009.tar.gz/download


ChimeraSlayer, on the other hand, has undergone some more serious improvements.  Its accuracy with short reads (down to 200 bp chimeras) is greatly improved, particularly with divergent chimeric sequences, due to including a chimera-specific realignment step introduced between the chimeric parent-identification stage and the CSlayer bootstrap support calculations.  NAST-iEr, by default, does not generate high quality alignments with divergent chimeric sequences.  This new intermediate realignment step leverages the parent sequences selected in the parent identification step (chimeraMaligner) to do a NAST-iEr profile-based realignment of the query, yielding a more meaningful NAST-formatted alignment and subsequently leading to higher ChimeraSlayer sensitivity on such sequences.  It matters most with short reads; long sequences are largely unaffected and have high chimera detection sensitivity with/without this step... the realignment is very fast and so doesn't hinder performance by including it as a default part of the process.  Just be sure to have NAST-iEr installed before running the new version of ChimeraSlayer, since it now depends on it.

A manuscript is in the works that describes this tool suite and its application on various sequence collections.

Regards,

-Brian (on behalf of the Broad Institute microbiome group)