[mira_talk] Sanger capillary reads - chromatograms for EdIt sequence editor?
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 29 Nov 2011 11:07:45 +0000
Dear all,
I have some "Sanger" ABI capillary reads (*.ab1 files) I'd like
to assembly for a small genome. I have read:
http://mira-assembler.sourceforge.net/docs/chap_sanger_part.html
The MIRA manual talks about the EdIt automatic Sanger
sequence editor from Thomas Pfisterer which was trained
on ABI and ALF traces:
http://mira-assembler.sourceforge.net/docs/chap_intro_part.html#sect_intro_automatic_editors
Does this editor need the chromatogram trace data to work?
Or does it work purely at the sequence level (so FASTQ or
FASTA+QUAL would be equally fine)?
Apologies if this is covered somewhere in the manual,
but if it is I missed it or didn't understand.
Thanks,
Peter
P.S.
MIRA doesn't support ABI files, but apparently does read
SCF (the Staden trace file format), so I could probably
convert my *.ab1 files into *.scf if that helps.
I know how to convert ABI files into FASTQ or FASTA+QUAL,
and that the default base calls by the ABI software can be
improved upon (e.g. using the open source tool tracetuner).
I also have the primer sequences so could trim those.
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