[BiO BB] Getting better assemblies from phrap
marty.gollery at gmail.com
Wed Sep 5 17:19:39 EDT 2007
You might investigate other basecalling software, such as KB,
PeakTrace and LongTrace.
On 9/5/07, Amir Karger <akarger at cgr.harvard.edu> wrote:
> 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
> General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org
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