Dear Bastien, We have been using MIRA for 454 transcriptome sequences assembly for a while. This is the first time we use the new version (version3.2.1) to assembly one full plate of 454 titanium normalized EST data. Surprisingly, there is no singlet in the output! Everything has been assembled to contig. The command we used for the 454 EST assembly: /nfs/bio/sw/bin/mira -project=ISI -fasta -job=denovo,est,accurate,454 -noclipping -notraceinfo 454_SETTINGS -AS:mrl=50 -AL:mrs=94 -OUT:sssip=yes -CL:bsqc=yes. I checked the manual and saw this part: "-OUT:sssip=yes" which I assume this should send all singlets to the results, and it's the same command I used before for other EST 454 sequencing assembly project with the old version . So I can not explain why there is no singlets for this assembling. Don't know whether the new version is the reason. I will really appreciate your answer for this. Thanks Zhao