Hi Bastien, Thank you for you reply. We are currently using mira to assemble cDNA (EST) sequences which should be low coverage of the transcriptome. If I switch off the -CL:pec as you recommended, we found that quite a few sequences not assembled together only differ in a short stretch of the ends (which are usually in relatively low quality). If I switch on, then the information of a lot of alternative splicing will be lost. Hope you can add this function to mira and thank you so much. Yi -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html