We are pleased to be releasing mothur v.1.19.0; however, we wish it were under better circumstances. Recently it came to our attention that the testing approach we were using to measure our ability to detect true chimeras (sensitivity) while limiting the risk of falsely calling sequences chimeric (specificity) was flawed. It turns out that while we had significantly increased the sensitivity compared to the original version of ChimeraSlayer (http://microbiomeutil.sourceforge.net/), we also increased the false positive rate. For example, using the test set available with the original ChimeraSlayer on test sequences that were 200 bp, the sensitivity increased from 63% to 70% and the specificity decreased from 99.4% to 87.4%. With longer sequences the difference in sensitivity and specificity increases. This approach to measuring specificity is conservative; however, it is much more reliable than what we had been doing. In summary, while chimera.slayer did a better job of identifying true chimeras, it also mistakenly called many good sequences chimeric. The practical upshot is that it if you used the default settings in chimera.slayer it is likely that extra sequences were removed. Since learning of this problem, we have been trying to modify our version of chimera.slayer to be more faithful to the original ChimeraSlayer. At this point, the main differences between ours and the original is the ability to use any reference alignment and significantly improved speed. We are removing the distance and kmer search methods for the time being and will do as the original does and use megablast to do the parent searching.
This is a pretty critical update and insist that everyone update their version of mothur. Please spread the word to colleagues that have not received this notice. We know you trust us to give you a robust and reliable software package and hope you can accept our apology for any problems this may cause in your analysis. Feel free to contact Pat if you have any question, concerns, or flames.
- chimera.slayer - significant overhaul to make it more faithful to the original ChimeraSlayer program
- screen.seqs - added qfile parameter
- get.current - now displays the current number of processors and flow file type is now saved with the current feature
- filter.seqs, align.seqs, etc. - current can now be used in a list of file names. example - fasta=current-silva.gold.align now works.