sequence assembly
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DNA contig assembly


A Command-Line DNA Sample Converter

An affordable alternative to the really expensive software for DNA sequence assembly and contig editing.

sequence assembling software


Program description


Convertrix is a molecular biology command line tool for converting between several popular DNA sample formats. It can automatically trim the untrusted regions (low quality bases) at the end of samples.


The following formats are supported:




Instant download


This tool is delivered in the DNA Baser package. Click the download button to get this package.


Convertrix - A Batch DNA Sample Converter

Version 1.0
Download size
~0.9 MB
Download time

less than 3 seconds

OS: Windows Microsoft Windows
DNA Sequence Assembler-Microsoft Windows download




  • Can be used in scripts to convert thousands of files
  • GUI to help you to generate the command line
  • Automatically trim untrusted regions
  • Formats: FASTA, SCF, SEQ, TXT, GBK, ABI
  • Doesn't need to be installed/uninstalled
  • Very small (less than 1MB)
  • Portable


Quick links






100% virus free All programs have been scanned against viruses


How to use it


You don't have to read a manual in order to use this program. A graphic interface is available to help you to generate the command line.

The same program acts both as a GUI and command line tool. The difference is made by the way you start the program:

  1. Command Line Generator (graphic) mode: double click program's icon.
  2. Format Converter: start the program from a DOS box/DOS script and pass some arguments into the command line

Fig 1 - Convertrix running in GUI mode



Fig 2 - Convertrix running as 'sample format converter'



Supported command line switches:

  Switch Description
The input sample. The following input formats are supported: SCF, ABI, FASTA, SEQ, TXT, GBK.
  --outputfolder The folder where the output file will be written. Default=application's folder.
  --trimends The program will automatically trim low quality ends (if the input sample has confidence score info embedded).
  --writelog Write details about how the conversion went. Useful to see possible errors you may have during conversion. The log will be written in the output folder.
  --outputformat The following output formats are supported: SCF, FASTA, SEQ, TXT, GBK.
  --windlength WindowLength parameter for trimming engine.
  --goodconfidence scoretresh Goodconfidence scoreTresh parameter for trimming engine.
  --goodbasesno GoodBasesNo parameter for trimming engine.

Note: You don't have to write theses switches by hand in your script file. Let the GUI to generate them for you.



Example of scripts


How to convert all SCF files in a folder to FASTA:


Let's say that you have 1000 SCF sample file in the 'c:\samples' folder and you want to put the output (FASTA format) in the 'c:\samples\output' folder.

Create a new text file with Notepad and copy the code from the black box below in it. Save the file as 'convert_all.cmd' and double click it to execute it. In few seconds you will have all SCF files converted to FASTA.



for %%F IN (c:\samples\*.scf) DO Convertrix.exe --InputFile="%%F" --OutputFormat=fasta --OutputFolder="c:\samples\output" --enable-TrimEnds --enable-WriteLog





How to install it

Convertrix Sample Converter is delivered in a small package together with other free molecular biology tools. Download the package and double click it. The programs inside the package will be extracted to the destination folder (specified by you). Go to the destination folder and double click the program you want to use.

This software tool installs in any computer even if you don't have administrator rights.




Convertrix is really small so you can easily copy it on a floppy disk or USB flash stick and take it with you.



System requirements


Convertrix can run on any version of Windows from Windows 98 to Windows 7 and also on Mac via Parallels or Bootcamp. It does not install additional libraries, updates, DLL, Java or registry keys into your system.



Full list of molecular biology tools


Name   Description
DNA Sequence Assembler
DNA Sequence Assembler
DNA Baser is a tool for DNA sequence assembly, DNA sequence analysis, contig editing, and mutation detection. It also offers a powerful chromatogram viewer/editor.
GBK to FASTA converter
GBK to FASTA converter freeware
GenBank to FASTA is a freeware program will convert GenBank (gbk) file format to FASTA format.
ABI to FASTA converter
ABI to FASTA Converter
ABI to FASTA Converter is a free tool will convert all (selected) ABI files to FASTA files. All you need to do is to locate your ABI chromatogram files and press the CONVERT button.
Grid cell counter
Grid cell counter Gird cell counter will help you to count faster the cells shown on computer's screen by displaying a grid over your image. Freeware.
A Batch DNA Sample Converter Convertrix is a molecular biology command line tool for converting between several popular DNA sample formats. It can automatically trim the untrusted regions (low quality bases) at the end of samples.
DNA Counter
DNA Counter DNA Counter shows the proportions between nucleotides in a DNA sequence (GC to AT ratio).
Chromatogram Explorer
multi-FASTA to FASTA

DNA Chromatogram Explorer is a Windows Explorer clone dedicated to DNA sequence analysis and manipulation. You can view the chromatograms while browsing through folders using its integrated file explorer. With a single click you can trim the low quality bases at the end of your samples.

Everything to FASTA converter
multi-FASTA to FASTA

Everything to Fasta Converter converts the specified samples (SCF, ABI, FASTA, multiFasta, GBK, multiGBK, SEQ, TXT) to FASTA format. Starting with version 3.0 protein FASTA files are also supported.



contig assembly software
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