[Biojava-l] ABI raw data files support?

[Ryan Golhar]

There is a program called Phred that is able to read the .ab1 files and
convert them into sequence files.

It can do this either without modifying the read so it appears "as is", or
to discard bases that cannot be determined.

In fact, I'm using Phred in a program to generate the raw sequence files,
and the "phred" sequence files as well.



-----Original Message-----
From: biojava-l-admin@biojava.org [mailto:biojava-l-admin@biojava.org]On
Behalf Of Schreiber, Mark
Sent: Tuesday, August 13, 2002 7:01 PM
To: David Atlan; biojava-l@biojava.org
Subject: RE: [Biojava-l] ABI raw data files support?


Hi -

This could be your lucky day.

There seems to have been a recent check in of a Class called ABI trace
in org.biojava.bio.program.abi.ABITrace that has the ability to read ABI
data. To get at this class you will need to checkout biojava-live from
the CVS. Its marked as version 0.5 alpha so you may need to do some
testing on it.

- Mark


> -----Original Message-----
> From: David Atlan [mailto:atlan_D@web.de]
> Sent: Wednesday, 14 August 2002 10:37 a.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] ABI raw data files support?
>
>
> Hi,
>
> I have been searching for a library, ideally in Java, that
> helps me to read ABI (3100, 3700) raw data files (.ab1). I
> went through the tutorial and the API, but could not find
> anything. EMBOSS seems to have something in C, but as I said,
> I am looking for Java.
>
> Is there something out there?
>
> Thanks a lot,
>
> David Atlan
> PS: I just registered on the mailing list, so I hope I can
> get the answer through it.
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