[mira_talk] Re: Assembly of high coverage genome

  • From: Andrej Benjak <abenjak@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 22 Sep 2016 08:59:45 +0200

Hello,

Well, the warning message said it all, the coverage was too high, and forcing it might have caused the erroneous assembly.

Try the same with half of the reads and see what happens.

Cheers,

Andrej


On 22-Sep-16 08:45, Bobby Paul wrote:

Respected Sir,

I am trying to assemble bacterial genome and MIRA shows an error and it aborted.

Manifest file and info file attached for your kind perusal.

Further I tried with using the parameter -NW:cac=no. It generated an assembly with double of the expected genome size.

1. Can you please suggest genome improvement strategies.
2. Is there any wrong in manifest file?
3. BLAST (pairwise) results of contigs from second assembly (with parameter -NW:cac=no) showing that many of the contigs have significant similarity. Is there any option to remove such duplicates?


Thanks and Regards
Bobby Paul



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