Hello, I am trying to assemble a genome with an estimated size of 3.8M. I have used allpath and generated an assembly. As a comparison, I'm trying to use MIRA assembler. I have 4 million 454 PE reads and 120 million Solexa reads. I have screened out adaptors by using SSAHA2. I then subset Solexa reads to 2.5 million and 454 reads to 400K, which is ~42x coverage for each of the platform. I then ran MIRA hybrid denovo assembly: mira --project=test --job=denovo,genome,normal,454,solexa The resulting contig stats seem to be really fragmented, see stats below. What can I do to improve scaffolding? My allpath assembly generated 15106 contigs, 11965 scaffolds, N50 contig size 1.9kb, which seems to be much better. Thanks for the help. All contigs: ============ Length assessment: ------------------ Number of contigs: 124259 Total consensus: 46425879 Largest contig: 4936 N50 contig size: 402 N90 contig size: 240 N95 contig size: 206 Coverage assessment: -------------------- Max coverage (total): 298 Max coverage per sequencing technology Sanger: 0 454: 304 IonTor: 0 PacBio: 0 Solexa: 767 Solid: 0 -- 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