[BiO BB] Getting better assemblies from phrap

[Diego Martinez]

Hello Amir,

what level coverage X is that at?

Diego
 
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----- Original Message ----
From: Amir Karger <akarger at CGR.Harvard.edu>
To: bio_bulletin_board at bioinformatics.org
Sent: Wednesday, September 5, 2007 11:23:48 AM
Subject: [BiO BB] Getting better assemblies from phrap

I've got a client who did a bunch of shotgun sequencing of a 100kb BAC
insert, and is now trying  to build an assembly with phredPhrap. He got
350 contigs. One was 12k, several were a few kb. We tried running with
-forcelevel 5, but that didn't help at all.

 

Are there other parameters that magically make phredPhrap work better?
I'm sure it depends on the quality of the reads. Many of them have at
least a region of good quality. There's a very long tail on a lot of
that, but the phred documentation says not to use the -trim option that
would remove those (and indeed phrap builds contigs even though the long
bad-quality tails don't match each other). Is there some way to tell
whether I have good enough quality? Is it not unusual to get just 12k,
and he'll just need to use primers suggested by consed to fill in gaps?

 

I'd appreciate any suggestions.

 

-Amir Karger

Research Computing Group

Life Sciences Division

Harvard University

akarger at cgr.harvard.edu

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