Banana Slug Genomics

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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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