[Bioperl-l] How to assess sequencing quality with Bioperl?

Nathan Haigh n.haigh at sheffield.ac.uk
Fri Sep 2 05:01:26 EDT 2005

I'm sure other people will have better, more indepth help, but to get you
started, I can point you in the right direction - but I haven't had to deal
with trace files myself - yet!

You will need to use Bio::SeqIO. The following HowTO shows the supported
formats inc. trace file formats: http://bioperl.org/HOWTOs/html/SeqIO.html. 

Have a read through the Bio::SeqIO.pm file, there is mention of needing to
install the Staden "io_lib" package, as well as the Bio::SeqIO::staden::read
package available from the bioperl-ext repository.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Andrew Leung
Sent: 02 September 2005 05:02
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] How to assess sequencing quality with Bioperl?

How to read trace files and report sequencing quality using Bioperl? Is
there anyone who can give me some hints on what Bioperl modules I can use
and what I could obtain from using them? I've googled the Bioperl site for
this topic, but felt fluctuated.
Thank you in advance.

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