From: Dan Bolser <dan.bolser@gm...> - 2010-12-16 09:03:15
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
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:
I think you can find what you're looking for here:
All the best,
2010/12/16 朱英杰 <zhyyjj_811@...>:
> 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