New versions of ChimeraSlayer, WigeoN, and NAST-iEr are released on sourceforge at:
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:
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.
-Brian (on behalf of the Broad Institute microbiome group)