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Old 10-13-2015, 03:38 AM   #15
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 824
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Quote:
Originally Posted by Brian Bushnell View Post
Let me know how the results are (good or bad); I've only assembled 1 virus with it and we still are not sure why other assemblers had so much trouble.
For a first-pass effort, I tried just assembling after only trimming (i.e. no host sequence filtering), working off MiSeq 250bp paired-end data:

Code:
tadpole.sh in=trimmed_NZGL01795_both_1P.fq.gz in2=trimmed_NZGL01795_both_2P.fq.gz  out=extended.fq mode=extend el=50 er=50 k=31 ecc=t
Unfortunately there were no extended sequences >400bp, so it looks like I'll need to do a bit of work to get a sequence out of these data.
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