An open source chimera checker for the fungal ITS region
R. Henrik Nilsson, Kessy Abarenkov, Vilmar Veldre, Stephan Nylinder, Pierre De Wit, Sara Brosche, Martin Ryberg, Erik Kristianson
(Molecular Ecology Resources, in press)

The pipeline, released under the GNU-GPL version 2 licence: download.

August 15, 2009: Initial release. V1.0
August 22, 2009: Minor cosmetic fix for Linux systems. V1.01
February 27, 2010: Slight enhancement of performance. V1.02
May 5, 2010: Minor enhancements. V1.1

The seed of the BLAST database: download (last updated on August 10, 2010).
(Not needed to run the software. This is a non-mandatory update of the BLAST database.)

The most time-consuming step of the program is the generation of multiple alignments of the sequences
found to be potentially chimeric and their 15 (default) best BLAST matches. By default the program uses linsi,
the most advanced mode of MAFFT, to do the alignment; this takes perhaps 30 seconds. You can gain a lot of
speed if you use another, faster MAFFT mode instead. The downside is that you sometimes miss the accuracy
of linsi. But if your sequences run in the tens of thousands, consider trying fftnsi or nwnsi instead.

Contact information

Henrik Nilsson (henrik dot nilsson at dpes dot gu dot se)
University of Gothenburg
Department of Plant and Environmental Sciences
Box 461
405 30 Gothenburg