Ok guys, problem solved using fasta2frag.tcl //www.freelists.org/post/mira_talk/Mapping-denovo-contigs-with-Reference,2 Felipe Lira Spanish National Center of Biotechnology - CNB/ CSIC Microbial Biotechnology Department Fellow of http://obrasocial.lacaixa.es/ Antes de imprimir este mensaje piense bien si es realmente necesario hacerlo. Before you print this e-mail, think well if it is really necessary. El Miércoles 20 de agosto de 2014 12:58, Felipe Lira <felipelira3@xxxxxxxxxxxx> escribió: Sorry. The e-mail subject would be CONTIGS, not READS Felipe Lira Spanish National Center of Biotechnology - CNB/ CSIC Microbial Biotechnology Department Fellow of http://obrasocial.lacaixa.es/ Antes de imprimir este mensaje piense bien si es realmente necesario hacerlo. Before you print this e-mail, think well if it is really necessary. El Miércoles 20 de agosto de 2014 12:56, Felipe Lira <felipelira3@xxxxxxxxxxxx> escribió: Hi Bastien! Is there any way to turn over the message above? I made a assembling with almost 100x coverage and the contigs size, in some cases, are over 20000nt. There are 181 contigs with different lengths. Trying to map these contigs against an annotated genome the program crashed. Bests, Felipe Lira Spanish National Center of Biotechnology - CNB/ CSIC Microbial Biotechnology Department Fellow of http://obrasocial.lacaixa.es/ Antes de imprimir este mensaje piense bien si es realmente necesario hacerlo. Before you print this e-mail, think well if it is really necessary.