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--- 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
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-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.

Banana Slug Genomics

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