Banana Slug Genomics

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Second test of [[bioinformatic_tools:mira|MIRA]] on campusrocks with Pog data. It was done as a follow up to [[computer_resources:assemblies:mira:pog: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:
  * 381266 reads assembled 
  * 2810480 bases assembled (2463546 if you ignore small contigs)
  * 31 contigs larger than 500 bps
  * n50: 490492 (490492 if you ignore small contigs)

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.

Banana Slug Genomics

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