[Bioperl-l] about hawkeye

Dan Bolser dan.bolser at gmail.com
Thu Dec 16 04:03:11 EST 2010


Hi Yingjie,

I'm replying to the AMOS-help and BioPerl mailing lists so that your
question can reach the largest audience of domain experts.

I believe there are tools within BioPerl that can convert SAM to
AMOS's AFG and bank formats, however, I haven't looked into those
recently.

Alternatively, you can open a SAM or an indexed BAM file in the Tablet
assembly viewer: http://bioinf.scri.ac.uk/tablet/

Finally, you can try asking your question (or searching for the
answer) on the SEQanswers forum: http://seqanswers.com/


About the broken link to the AMOS AFG format specification, recently
the AMOS manual was moved onto a wiki hosted on sourceforge.
Unfortunately they didn't set up a forwarding rule to allow the old
URLs to keep working. When you find a broken link to the AMOS manual,
try searching for the information here:

http://sourceforge.net/apps/mediawiki/amos


I think you can find what you're looking for here:

http://sourceforge.net/apps/mediawiki/amos/index.php?title=Infrastructure#File_format_specs


All the best,
Dan.

2010/12/16 朱英杰 <zhyyjj_811 at 163.com>:
> Dear Bolser,
>
> It is my great pleasure when you see this letter. Recently I use hawkeye
> visualization tools to view my assembly results. But I have some BAM or SAM
> format files. I need to convert BAM or SAM to AFG. Do you have a tools do
> it? Or I want to develop this conversion tool.Can you help me?
>
> I can't open this link about AFG formt,
> http://amos.sourceforge.net/docs/specs/. Can you send it to me?
>
> Thank you for your help!
>
> Best regards,
>
> Yingjie Zhu
> Institute of Medicinal Plant Development in Beijing, China
> 2010-12-17
>
>
>



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