sequence assembly
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scf trace assembly
DNA contig assembly
DNA Sequence Assembler
The only command line sequence assembler for Windows!



This tool is the command line version of the famous DNA Sequence Assembler. With this tool you can perform DNA sequence assembly from your own "DOS" (Windows console) and Linux scripts. .




  • import samples in the specified folder
  • automatically trim low quality ends
  • assemble the contig (it can also assemble to a reference sequence)
  • remove recognition (primer/vectors) sequences from contig
  • correct the ambiguities in contig
  • save the log and the contig to disk


Command line options


You can specify the following parameters:

  • Reference file
  • Input folder
  • Input file type (scf, abi, ab1, ab, fasta, seq, gbk)
  • Output folder
  • Recognition sequence - used to recognize and clean primers/vectors
  • Keep/Cut recognition sequence
  • Low quality end trimming
  • WriteLog



Example of script (create a BAT/CMD file and paste this code in it):


BaserConsole.exe ^
   /InputFolder="c:\samples" ^
   /FileType='*.abi' ^
   /OutputFolder="c:\samples\out" ^

pause > nul


This simple script will call DNA Baser Console using 'c:\samples' as input folder. All ABI samples in that folder will be assembled.



Name DNA Sequence Assembler Console v4.33
Date 30 March 2016
File size (single EXE file) ~ 3 MB
Download time less than 5 seconds
SFF converter - Free download





Known issue: the vector removal is not ready yet in this version, but we will have an update in the next 2 days.
What's new in this version...

News: Speed improvement. The assembler engine has been upgraded from DNA Baser v3 to DNA Baser v4.30. The "--TrimEnd parameter is ignored" bug has been fixed.

What's in the package/How to install it...

DNA Sequence Assembler Console 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.

DNA Sequence Assembler Console installs in any computer even if you don't have administrator rights. To uninstall DNA Sequence Assembler Console, just delete it.


This software tool is really small so you can easily copy it on a floppy disk or USB flash stick and take it with you or send it to your colleagues via email.

Instant feedback...

This tool is sequence analysis command line software. Please help us make it better. Let us know if you have any feature requests and we will try to integrate them.


Your feedback is important to us!



Similar bioinformatics tools included in this package


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 tool will convert all (selected) ABI files to FASTA files. All you need to do is to locate your ABI chromatogramfiles 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.



sequence assembling software
contig assembly software