On May 23, 2011, at 20:14 , Evan wrote: > I'm doing a solexa mapping assembly of paired end reads and the new data > building onto my backbone contigs is labeled in one of the following 2 > formats: > "_cer_sxa_214" > "ILLUMINA-2F52BD_0038:8:4:18110:7690#0/2" > And because its paired end data I can't very well do scaffolding with the > "_cer_sxa_214" data so how can I ensure that all my reads retain their > original names of "ILLUMINA-....." For what CER reads are, consult the documentation. But if you do not want them, use -CO:msr=no. Warning: memory usage and file size on disk will increase, sometimes dramatically so. Question from my side: would an option to keep reads at contig ends unmerged be something of interest to you? B.