Question: How can i get or generate Sanger .ab1 files?
0
gravatar for jawhar.saks
16 months ago by
jawhar.saks10
France
jawhar.saks10 wrote:

Hello,

I created a software working on abif batch files from Sanger sequencing.

I want to test it on a big amount of data to hunt for bugs, and for that i need a lot of data.

That's why i'm looking for .ab1 files generator, or sample/anonymous .ab1 files maybe.

I would like to get them with mutations, double, triple peaks and/or errors to be able to test my workflow properly.

I found out for now :

  • We can generate Fasta + quality with mason that simulates sanger files but don't give the .ab1 files.
  • We can Get trace data SCF format on NCBI and maybe convert them to .ab1, but I couldn't find sufficient files.
  • We can modify an .ab1 file using perl Bio::Trace::ABIF module or R sangerseqR maybe. This could work, but to get a lot of data examples, it will take quite a moment to change all and represent all cases that seams problematic...

Thank you for your time.

generate ab1 sample files sanger • 1.0k views
ADD COMMENTlink written 16 months ago by jawhar.saks10

UPDATE : I found out a few sequence on another post but not enough to be representative here : AB1 Files free download

ADD REPLYlink written 16 months ago by jawhar.saks10

There is only two software programs that can write .ab1 files and that is ABI's basecallers (KB & ABI) and our PeakTrace Basecaller. The reason it is so difficult to write .ab1 files is the format is not fully described and has lots of idiosyncrasies that result from the file format being in use back to the ABI 373 DNA sequencer (we are taking the 1980s!). We have found that not even ABI understands the .ab1 file format in full as different versions of their software produce different and incompatible .ab1 files.

The long and the short is that it is very, very hard to create a full .ab1 file from scratch and even if you do there are different versions produced by different versions of the ABI software. You might want to get in touch with me if you want a wide range of .ab1 files.

ADD REPLYlink written 14 months ago by Daniel Tillett0
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