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Old 05-17-2011, 04:27 AM   #1
anli
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Default Assembly of 150bp paired-end reads

Hi.

I'm working on a project where we will try to assemble a ~2MB bacterial genome based on illumina data.

The run will be made on a GAII with 150bp long reads.
The reads are paired-end with an insert size of 400bp.

I have planned on running velvet for the assembly, and I have done some trials with another dataset and gotten some decent results.
The difference however is that my trial-set is 54bp reads.

Has anybody here tried using velvet for longer read lengths? What was you impressions? Did you end up using any other software?

Also, how was the quality of the 150bp reads? How much of it will be usable? I've looked around some and gotten both positive and negative feedback on the quality of 150bp read length runs.

Cheers
Anders
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Old 05-18-2011, 04:01 AM   #2
tonybolger
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Quote:
Originally Posted by anli View Post
Also, how was the quality of the 150bp reads? How much of it will be usable? I've looked around some and gotten both positive and negative feedback on the quality of 150bp read length runs.
Forward read: median Q30 and mean Q20 at the end.
Reverse read: about 10 bases worse, so median Q30, mean Q20 at pos 140, dropping fairly rapidly after that.

We lose about 15% of total bases filtering at Q15, 20% filtering at Q20.
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