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Old 02-16-2010, 08:10 AM   #1
Location: it

Join Date: Oct 2009
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Default velvet

Hi .. ..If the velvet denovo assembly was done with contamination (chloroplast sequences ), the N50 is aboout 15 times higher than the assembly with out chloroplast sequences.I was trying to find out the reason but I couldnt , if any one have idea of this please share..

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Old 02-17-2010, 09:16 AM   #2
(Jeremy Leipzig)
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i guess anything that introduces more ambiguity into the smaller contigs will raise the N50 provided they somehow push the smaller guys under the coverage cutoff? in addition you are probably adding some nicely sized chloroplast contigs.

btw can you send me some of your chloroplast sequences? I would really like to improve my N50s.
Jeremy Leipzig
Bioinformatics Programmer
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