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archive:computer_resources:assemblies:mira:pog:mira-assembly1

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archive:computer_resources:assemblies:mira:pog:mira-assembly1 [2010/05/12 19:00]
mpcusack
archive:computer_resources:assemblies:mira:pog:mira-assembly1 [2015/08/24 11:22]
217.73.208.143 ↷ Links adapted because of a move operation
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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 input 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. 
archive/computer_resources/assemblies/mira/pog/mira-assembly1.txt · Last modified: 2015/09/02 16:43 by ceisenhart