Minimal example

The only mandatory paramater you need to specify is 'InputFolder'.

Classic example

The script above will call DNA Baser Console using 'c:\samples' as input folder. All ABI samples/chromatograms in that folder will be assembled. The DNA Baser Console exactly as DNA Sequence Assembler: it will automatically import samples, automatically trim low quality ends, remove recognitions sequences, correct the ambiguities and save the log and the contig to disk (in the c:\samples\out' folder in this example).

Run sequence assembly at batch

If you want to assemble all sequences in 1000 folders you can do something like this:

Or better, you can use a FOR loop as shown here:

More details about the FOR loop here: https://stackoverflow.com/questions/138497/iterate-all-files-in-a-directory-using-a-for-loop

Help

At the console, type BaserConsole.exe /? to get help:

--inputfolder=path      Assemble samples in this folder

--outputfolder=path      Optional. The folder where the output file will be written (default=input folder)

--reference=file      Optional. The reference sample. Make sure it is located in a folder different than the input folder

--filetype=string      Optional. Assemble only the samples that have this extension. Example: '*.scf'. The following input formats are supported: SCF, ABI, FASTA, SEQ, TXT, GBK. (default: *.*)

--vectordb=file      Optional. Primer database file. This file can be generated with DNA Baser

--writelog=boolean      Optional. Write details about how the conversion went. The log will be written in the output folder (default: true)

--keepvector=boolean      Optional. Keeps of removes the vector from contig. (default=FALSE)

--trimends      Optional. The program will automatically trim low quality ends (if the input sample has QV info embedded) (default: true)

--goodbasesno=int      Optional. GoodBasesNo parameter for trimming engine (default: 60)

--windlength=int      Optional. WindowLength parameter for trimming engine (default: 16)

--goodqvtresh=int      Optional. GoodQVTresh parameter for trimming engine (default: 20)

--wordsize=int      Optional parameter for contig assembler. (default: 18)

--identproc=int      Optional parameter for contig assembler. (default: 65)

--minoverlap=int      Optional parameter for contig assembler. More details on our web site. (default: 20)

Known issues

The InputFolder and OutputFolder should not end with a backslash character (\).

Example:

        Accepted:       --InputFolder=C:\MySamples

        NotAccepted:  --InputFolder=C:\MySamples\