This shows you the differences between two versions of the page.
Next revision | Previous revision | ||
archive:computer_resources:assemblies:mira:pog:mira-assembly1 [2010/05/12 18:57] mpcusack created |
archive:computer_resources:assemblies:mira:pog:mira-assembly1 [2015/09/02 16:43] (current) ceisenhart ↷ Page moved from computer_resources:assemblies:mira:pog:mira-assembly1 to archive:computer_resources:assemblies:mira:pog:mira-assembly1 |
||
---|---|---|---|
Line 1: | Line 1: | ||
- | This was the first test of [[bioinformatic_tools:mira|MIRA]] on campusrocks. Pog data (with a known but not provided reference genome) was provided with mostly default options. Sanger and 454 data was used, but not SOLiD which is not supported by MIRA. | + | This was the first test of [[archive:bioinformatic_tools:mira|MIRA]] on campusrocks. Pog data (with a known but not provided reference genome) was input with mostly default options. Sanger and 454 data was used, but not SOLiD which is not supported by MIRA. |
+ | |||
+ | Mira was run with (mostly) default options and the command: | ||
+ | mira -project=pog -fasta -job=denovo,genome,normal,sanger,454 SANGER_SETTINGS -LR:wqf=no -AS:epoq=no | ||
+ | |||
+ | The extra sanger settings were needed because we lack quality information for those reads. With out these flags mira will fail when it realizes there are no quality files. | ||
+ | |||
+ | On this run, MIRA took approximately 10 hours to assemble. | ||
+ | |||
+ | faSize of the results: | ||
+ | 2800983 bases (120 N's 2800863 real 2800863 upper 0 lower) in 622 sequences in 1 files | ||
+ | Total size: mean 4503.2 sd 38654.6 min 48 (pog_c361) max 640220 (pog_c7) median 545 | ||
+ | N count: mean 0.2 sd 0.6 | ||
+ | U count: mean 4503.0 sd 38654.6 | ||
+ | L count: mean 0.0 sd 0.0 | ||
+ | %0.00 masked total, %0.00 masked real | ||
+ | |||
+ | Other summary information: | ||
+ | * 381179 reads assembled | ||
+ | * 30 contigs larger than 500 bps | ||
+ | * n50: 367811 (368219 if you ignore small contigs) | ||
+ | * | ||
+ | Overall it appears to be a decent assembly. The largest contig was 640k and there were only 30 significantly sized ones. | ||
+ | |||
+ | After blating it was discovered that one of the larger contigs was chimeric. Nothing in the logs or output indicated a problem with this contig and it showed average quality values. |