Answers.Body: <p><a href="http://www.dnabaser.com/download/download.html" rel="nofollow noreferrer">DNA Baser Assembler</a> will convert ABI to SCF (and other formats). 
  Just double click the ABI file you want to convert then go to the "Samples" menu and choose "Save current samples as...". Plus, it can automatically trim the low quality ends.</p>
  
  <p><a href="https://i.sstatic.net/7GvoY.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/7GvoY.png" alt="enter image description here"></a>
  There is another tool in that package what will convert all ABI files at batch: <a href="http://www.dnabaser.com/download/chromatogram-explorer/index.html" rel="nofollow noreferrer">Chromatogram Explorer</a>. There is a Lite version that is free, but the conversion to SCF might only work for the first 100 files (if I remember correctly).</p>
  
  <p>Related to the comment posted by BioGeek about the Genious license: DNA Baser Assembler does not require a license key. It will work right away.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-10-02T22:30:14.000Z
Answers.Text: The OP was asking for SCF->ABI I think your response is only SCF->ABI.  Do those tools work in both directions?
Answers.UserDisplayName: Bioathlete
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-10-02T18:01:32.747Z
Answers.LastActivityDate: 2018-10-02T18:13:03.940Z
Answers.LastEditDate: 2018-10-02T18:13:03.940Z
Answers.UserDisplayName: IceCold
Answers.Body: <p>Apparently <code>convert_trace</code> does not do a good parameter checking and silently sets ZTR as default if it does not recognise a valid output format.</p>
  
  <p>I don't know of any freely available command-line converters in that specific direction. Even at the height of Sanger sequencing (late 90s, early 2000s), pipelines usually tried to reduce complexity and footprint by converting AB1 to anything else, often SCF (ZTR came too late and never got enough traction).</p>
  
  <p>That being said, I dug out an SCF I had from 1997, loaded it into <a href="http://www.geneious.com/" rel="nofollow noreferrer">Geneious</a>, and re-exported it as .ab1. I was a bit astonished to see that this worked. So Geneious (or similar packages from other companies) may be your best bet for a quick, one-off thing.</p>
  
  <p>Depending on your needs, you might want to think about other ways: either expand BioPython to read SCFs, or maybe to expand the Staden io_lib to be able to write .ab1 (James still maintains that package and is extremely helpful).</p>
  
  <p>Good luck.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-15T11:20:39.410Z
Answers.Text: I downloaded Geneious and requested a trial license. I'm indeed able to import SCF files, but I don't see 'ab1' as an export format? So, I'm guessing that I will need to go with one of your other two options...
Answers.UserDisplayName: BioGeek
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-15T14:27:39.437Z
Answers.Text: I checked again and my version of Geneious (10.1.3) definitely offers an "ABI chromatogram (*.ab1)" as type in the "File->Export selcted document ..." dialog. Was your SCF selected?
Answers.UserDisplayName: BaCh
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Answers.CreationDate: 2017-06-13T14:06:16.443Z
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Answers.UserDisplayName: BaCh
Body: <p>I have a large collection of sequence trace files which are in <a href="http://staden.sourceforge.net/manual/formats_unix_2.html" rel="nofollow noreferrer">SCF file format</a> (binary files that in addition to the string of DNA bases also contain the electropherogram of the sample and quality information about the base calls).</p>
  
  <p>I have an existing BioPython pipeline that accepts files in <a href="http://www6.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf" rel="nofollow noreferrer">AB1 format</a> (pdf), so I need to convert my SCF files to AB1 files.</p>
  
  <p>I found a question on Biostars that asks for the opposite: <a href="https://www.biostars.org/p/622/" rel="nofollow noreferrer">converting from SCF to AB1</a>.</p>
  
  <p>The accepted answer there was to use <a href="http://staden.sourceforge.net/manual/manpages_unix_1.html" rel="nofollow noreferrer"><code>convert_trace</code></a> from the Staden package.</p>
  
  <pre><code>./convert_trace -out_format scf &lt; trace.ab1 &gt; trace.scf
  </code></pre>
  
  <p>So I tried the opposite:</p>
  
  <pre><code>./convert_trace -out_format abi &lt; trace.scf &gt; trace.ab1
  </code></pre>
  
  <p>This did indeed produce a file with <code>*.ab1</code> extension, but upon importing it to my BioPython pipeline, I got the error</p>
  
  <pre><code>File should start ABIF, not '\xaeZTR'
  </code></pre>
  
  <p>So apparently, <code>convert_trace</code> converted my files to <a href="http://staden.sourceforge.net/manual/formats_unix_12.html" rel="nofollow noreferrer">ZTR format</a>, even altough I specified <code>-out_format abi</code>.</p>
  
  <p>Closer reading of the manual states that <code>[convert_exe] can write CTF, EXP, PLN, SCF and ZTR formats.</code> (so indeed no ABI), but it confuses me why <code>ABI</code> is still a valid output format.</p>
  
  <p>So, my question is, how do I convert SCF files into ABI files?</p>
  
Tags: <format-conversion>
Title: How can I convert SCF trace files to ABI files?
ThreadText: # How can I convert SCF trace files to ABI files?
  
  (Asked by: username_0 on 2017-06-13)
  
  I have a large collection of sequence trace files which are in [SCF file format](http://staden.sourceforge.net/manual/formats_unix_2.html) (binary files that in addition to the string of DNA bases also contain the electropherogram of the sample and quality information about the base calls).
  
  I have an existing BioPython pipeline that accepts files in [AB1 format](http://www6.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf) (pdf), so I need to convert my SCF files to AB1 files.
  
  I found a question on Biostars that asks for the opposite: [converting from SCF to AB1](https://www.biostars.org/p/622/).
  
  The accepted answer there was to use [`convert_trace`](http://staden.sourceforge.net/manual/manpages_unix_1.html) from the Staden package.
  
  ```
  ./convert_trace -out_format scf < trace.ab1 > trace.scf
  
  ```
  
  So I tried the opposite:
  
  ```
  ./convert_trace -out_format abi < trace.scf > trace.ab1
  
  ```
  
  This did indeed produce a file with `*.ab1` extension, but upon importing it to my BioPython pipeline, I got the error
  
  ```
  File should start ABIF, not '\xaeZTR'
  
  ```
  
  So apparently, `convert_trace` converted my files to [ZTR format](http://staden.sourceforge.net/manual/formats_unix_12.html), even altough I specified `-out_format abi`.
  
  Closer reading of the manual states that `[convert_exe] can write CTF, EXP, PLN, SCF and ZTR formats.` (so indeed no ABI), but it confuses me why `ABI` is still a valid output format.
  
  So, my question is, how do I convert SCF files into ABI files?
  
  **Tags:** format-conversion
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2017-06-13. Score: 4 | Accepted answer
  
  Apparently `convert_trace` does not do a good parameter checking and silently sets ZTR as default if it does not recognise a valid output format.
  
  I don't know of any freely available command-line converters in that specific direction. Even at the height of Sanger sequencing (late 90s, early 2000s), pipelines usually tried to reduce complexity and footprint by converting AB1 to anything else, often SCF (ZTR came too late and never got enough traction).
  
  That being said, I dug out an SCF I had from 1997, loaded it into [Geneious](http://www.geneious.com/), and re-exported it as .ab1. I was a bit astonished to see that this worked. So Geneious (or similar packages from other companies) may be your best bet for a quick, one-off thing.
  
  Depending on your needs, you might want to think about other ways: either expand BioPython to read SCFs, or maybe to expand the Staden io\_lib to be able to write .ab1 (James still maintains that package and is extremely helpful).
  
  Good luck.
  
  > **Comments:**
  > **username_0**: I downloaded Geneious and requested a trial license. I'm indeed able to import SCF files, but I don't see 'ab1' as an export format? So, I'm guessing that I will need to go with one of your other two options...  
  > **username_3**: I checked again and my version of Geneious (10.1.3) definitely offers an "ABI chromatogram (*.ab1)" as type in the "File->Export selcted document ..." dialog. Was your SCF selected?  
  
  ---
  
  ### Answer by username_1 on 2018-10-02. Score: 1
  
  [DNA Baser Assembler](http://www.dnabaser.com/download/download.html) will convert ABI to SCF (and other formats).
  Just double click the ABI file you want to convert then go to the "Samples" menu and choose "Save current samples as...". Plus, it can automatically trim the low quality ends.
  
  [![enter image description here](https://i.sstatic.net/7GvoY.png)](https://i.sstatic.net/7GvoY.png)
  There is another tool in that package what will convert all ABI files at batch: [Chromatogram Explorer](http://www.dnabaser.com/download/chromatogram-explorer/index.html). There is a Lite version that is free, but the conversion to SCF might only work for the first 100 files (if I remember correctly).
  
  Related to the comment posted by username_0 about the Genious license: DNA Baser Assembler does not require a license key. It will work right away.
  
  > **Comments:**
  > **username_2**: The OP was asking for SCF->ABI I think your response is only SCF->ABI.  Do those tools work in both directions?  
  
  ---
  
  