[mira_talk] Re: Beginner Question RE sanger data in hybrid assembly
- From: Sven Klages <sir.svencelot@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 23 Nov 2009 21:29:10 +0100
Hi Jeremiah,
you should basecall the ab1 data (not only extracting the sequence from the
abi file).
There are two (common) basecalling programs:
1) phred (http://www.phrap.org/consed/consed.html#howToGet)
2) TraceTuner (https://sourceforge.net/projects/tracetuner/)
Both produce sequences in fasta format with qualities ...
You should also get rid of vector / low quality ranges.
For sanger data lucy is doing a good job (
https://sourceforge.net/projects/lucy/).
Lucy itself writes only offsets, you need to clip your files accordingly by
yourself.
As an alternative you can use lucy2 (
http://www.complex.iastate.edu/download/Lucy2/index.html)
which is the lucy clipping program with a graphical user interface and which
clips the reads physically,
not only dumps offsets.
After basecalling and vector/lowquality clipping you can go for MIRA ..
cheers,
Sven
2009/11/23 Jeremiah Davie <jdavie@xxxxxxxxxxx>
> Hi All,
> I am learning to use MIRA and wanted to incorporate Sanger data along
> with a 454 run. The problem is that the sanger data is saved as *.ab1 files,
> as the sanger sequencing facility at our university uses an older ABI
> sequencer. I can use Sequencher to convert those files to fasta/fastq files,
> but cannot generate the traceinfo.xml files that MIRA expects. Is there a
> way to avoid using the traceinfo.xml files? Conversely, does anyone know of
> a program that will convert an .ab1 file to fasta/fastq/traceinfo.xml
> collection? If not, can someone guide me to an easy to follow guide for
> writing a traceinfo.xml file? Any help would be greatly appreciated; I'm
> pulling my hair out on this. Sincerely, Jeremiah
>
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