[BiO BB] Getting better assemblies from phrap

[Martin Gollery]

Hi Amir,

You might investigate other basecalling software, such as KB,
PeakTrace and LongTrace.

Cheers,
Marty


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
>
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>


-- 
-- 
Martin Gollery
Senior Bioinformatics Scientist
TimeLogic- a Division of Active Motif
775-833-9113
880 Northwood Blvd. Suite 7
Incline Village, NV 89451