New versions of ChimeraSlayer, WigeoN, and NAST-iEr are released on
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,
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)
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