Answers.Body: <h2><a href="https://trace.ncbi.nlm.nih.gov/Traces/trace/trace.cgi?view=list_arrivals" rel="nofollow noreferrer">NCBI Trace Archive</a></h2>
  <p>The NCBI Trace Archive is a permanent repository of DNA sequence chromatograms (traces), base calls, and quality estimates for single-pass reads from various large-scale sequencing projects. Contaning more than 2 billion traces.</p>
  <p><a href="https://i.sstatic.net/z95Hu.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/z95Hu.png" alt="![![enter image description here" /></a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-08-24T18:21:23.993Z
Answers.LastActivityDate: 2021-08-25T14:42:21.503Z
Answers.LastEditDate: 2021-08-25T14:42:21.503Z
Answers.UserDisplayName: alex3465
Body: <p>I am looking for any public available databases where I can download Sanger <a href="http://www.dnabaser.com/help/samples/what%20is%20a%20chromatogram.html" rel="nofollow noreferrer">chromatography</a> data ideally in <a href="https://www.reviversoft.com/en/file-extensions/ab1" rel="nofollow noreferrer">Ab1</a> or <a href="http://staden.sourceforge.net/manual/formats_unix_2.html" rel="nofollow noreferrer">SCF</a> file format. I need extremely large amounts of this, since I want to use it for machine learning.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-08-18T14:13:18.387Z
Comments.Text: @ATpoint , can you link me here any ML based solution for basecalling if you know any ? I found only 2-3 papers in the literature
Comments.UserDisplayName: alex3465
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-08-18T19:10:49.047Z
Comments.Text: Why do you want to reinvent the wheel on this? This is an old technology that doesn't require any new tools, not least of which because its use is decreasing every year.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-08-18T21:57:27.303Z
Comments.Text: @DevonRyan I can fully unterstand what do mean but Sanger DNA sequencing is not going away any time soon, also we are looking for inhouse Basecalling method/software which will be independent of any licencing
Comments.UserDisplayName: alex3465
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-08-19T10:12:51.527Z
Comments.Text: I must agree with the others. Furthermore, I'd say writing a script that can deal with frameshifted sequences in the PCR pool (the major issue with basecalling) is easier, but that is application specific as in general Sanger is used for validation and the data has to be perfect. E.g. I wrote a [tool to call secondary peaks](https://direvo.mutanalyst.com/main/mutantcaller) to test the diversity of error prone PCR pools, which is a super specific application.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-08-19T10:16:09.200Z
Comments.Text: There are some interesting trends in a Sanger trace, i.e. peak height distribution, which tell you about how well the experiment was (concentrations, gunk etc.), but that again is not too interesting to be heavily used —unless say implemented in Benchling or other major tool, i.e. the tricky part of a new tool is getting to be adopted.
  Furthermore, about licensing the Ab1 files are what is spat out by the machine and that is where the licensing/compression comes into play, not in basecalling as one can very easily do the basecalling from the raw data within them ignoring the calls.
Comments.UserDisplayName: Matteo Ferla
Tags: <ngs><sequence-analysis><public-databases><data-download>
Title: Where to find publicly available Sanger chromatography data?
ThreadText: # Where to find publicly available Sanger chromatography data?
  
  (Asked by: username_0 on 2021-08-18)
  
  I am looking for any public available databases where I can download Sanger [chromatography](http://www.dnabaser.com/help/samples/what%20is%20a%20chromatogram.html) data ideally in [Ab1](https://www.reviversoft.com/en/file-extensions/ab1) or [SCF](http://staden.sourceforge.net/manual/formats_unix_2.html) file format. I need extremely large amounts of this, since I want to use it for machine learning.
  
  **Tags:** ngs, sequence-analysis, public-databases, data-download
  
  > **Comments:**
  > **username_0**: @ATpoint , can you link me here any ML based solution for basecalling if you know any ? I found only 2-3 papers in the literature  
  > **username_1**: Why do you want to reinvent the wheel on this? This is an old technology that doesn't require any new tools, not least of which because its use is decreasing every year.  
  > **username_0**: @username_1 I can fully unterstand what do mean but Sanger DNA sequencing is not going away any time soon, also we are looking for inhouse Basecalling method/software which will be independent of any licencing  
  > **username_2**: I must agree with the others. Furthermore, I'd say writing a script that can deal with frameshifted sequences in the PCR pool (the major issue with basecalling) is easier, but that is application specific as in general Sanger is used for validation and the data has to be perfect. E.g. I wrote a [tool to call secondary peaks](https://direvo.mutanalyst.com/main/mutantcaller) to test the diversity of error prone PCR pools, which is a super specific application.  
  > **username_2**: There are some interesting trends in a Sanger trace, i.e. peak height distribution, which tell you about how well the experiment was (concentrations, gunk etc.), but that again is not too interesting to be heavily used —unless say implemented in Benchling or other major tool, i.e. the tricky part of a new tool is getting to be adopted. Furthermore, about licensing the Ab1 files are what is spat out by the machine and that is where the licensing/compression comes into play, not in basecalling as one can very easily do the basecalling from the raw data within them ignoring the calls.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2021-08-24. Score: 2 | Accepted answer
  
  ## [NCBI Trace Archive](https://trace.ncbi.nlm.nih.gov/Traces/trace/trace.cgi?view=list_arrivals)
  
  The NCBI Trace Archive is a permanent repository of DNA sequence chromatograms (traces), base calls, and quality estimates for single-pass reads from various large-scale sequencing projects. Contaning more than 2 billion traces.
  
  [![![![enter image description here](https://i.sstatic.net/z95Hu.png)](https://i.sstatic.net/z95Hu.png)
  
  
  ---
  
  