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Old 06-25-2015, 04:56 AM   #8
maasha
Senior Member
 
Location: Denmark

Join Date: Apr 2009
Posts: 153
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I should say Biopieces is pretty nifty for this task:


https://code.google.com/p/biopieces/...embled_contigs

You simply do:

Code:
read_fasta -i contigs.fna |
grab -e "SEQ_LEN>=200" |
analyze_assembly -x
and get:

Code:
N50: 9082
MAX: 52038
MIN: 200
MEAN: 4170
TOTAL: 3057214
COUNT: 733
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