next gen sequencing

Jalview Discussion
1

hello,
is there any way to convert a .ace file generated from NGS to fasta, so that i can view the alignment in jalview.

thank you,
michelle

···

--
Michelle Simon
Bioinformatics,
MRC Mammalian Genetics Unit,
Harwell, Oxon, ox11 0rd, U.K.
E-mail: m.simon@har.mrc.ac.uk
Telephone: +44 (0)1235 841031
www: http://www.har.mrc.ac.uk/

2

Hi Michelle - sorry I haven't replied to your email earlier!
michy wrote:

hello,
is there any way to convert a .ace file generated from NGS to fasta, so
that i can view the alignment in jalview.

not that I know of - but it looks like its needed. Just to clarify, you
mean an .ace file such as generated by phrap - like the one here that is
documented here ?

http://bozeman.mbt.washington.edu/consed/distributions/README.15.0.txt
(search for 'ACE FILE FORMAT')

cheers,
Jim.

3

Hi Michelle.

I'm not sure if this is a perfect solution, but Andrew Waterhouse
suggested you try AMOS :

http://amos.sourceforge.net

You'll need to install the whole AMOS distribution to get the file
converters. The documentation says that there is a converter from .ACE
to AMOS, and from AMOS -> FASTA:
http://amos.sourceforge.net/docs/converters/#mozTocId764590

Not sure about quality and assembly statistics, but it looks like the
AMOS forensics package will generate gff files that you can load on to
the sequence (or view in Hawkeye - I guess!).

hope it helps
Jim

michy wrote:

···

hello Jim,
yes it is the same .ace file that you get from phrap, it would be great
if this could be converted to fasta and view in jalview. maybe it could
be added to this todo list.

thank you,
michelle

James Procter wrote:

Hi Michelle - sorry I haven't replied to your email earlier!
michy wrote:

hello,
is there any way to convert a .ace file generated from NGS to fasta, so
that i can view the alignment in jalview.
    

not that I know of - but it looks like its needed. Just to clarify, you
mean an .ace file such as generated by phrap - like the one here that is
documented here ?

http://bozeman.mbt.washington.edu/consed/distributions/README.15.0.txt
(search for 'ACE FILE FORMAT')

cheers,
Jim.
  
--
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J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
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