Second test of MIRA on campusrocks with Pog data. It was done as a follow up to mira-assembly1 which had a chimeric contig. Mostly default options were still used, but an extra flag was specified that forced MIRA to be more stringent and perform more iterations. Same as last time, Sanger and 454 data was used, but not SOLiD.
Mira was run with the command:
mira -project=pog -fasta -job=denovo,genome,normal,sanger,454 -highlyrepetitive SANGER_SETTINGS -LR:wqf=no -AS:epoq=no
On this run, MIRA took 774 minutes (12.9 hours) to assemble. An over 50% increase from not using the highlyrepetitive flag.
faSize of the results:
2795791 bases (122 N's 2795669 real 2795669 upper 0 lower) in 604 sequences in 1 files Total size: mean 4628.8 sd 49980.5 min 40 (pog_s574) max 1040104 (pog_c3) median 548 N count: mean 0.2 sd 0.6 U count: mean 4628.6 sd 49980.2 L count: mean 0.0 sd 0.0 %0.00 masked total, %0.00 masked real
Other summary information:
Appears to be a superior assembly. The largest contig was 1040k which is as good as any other de novo assembler tested.
No evidence of chimeric assembly.