Question: Looking For A Good Open Source Command-Line Sanger Sequence Pairwise Assembler
3
gravatar for Mike
6.9 years ago by
Mike80
Mike80 wrote:

I'm looking for a simple command-line program that will automatically assemble pairs of fairly long Sanger chromatographs. The assembly software solutions I've found are either extreme overkill for what I want to do (optimized for assembling millions of short next-gen reads) or GUI-only (Geneious or Sequencher). Phred/phrap would be the obvious answer, but it's non-free and closed-source and also pretty ancient. I'm not even looking to create publishable sequences -- just trying to use this as a QC step for DNA barcodes. Thanks!

sanger barcode • 3.0k views
ADD COMMENTlink modified 4.2 years ago by BioApps740 • written 6.9 years ago by Mike80

I had good results with Arachne and Celera :)

ADD REPLYlink modified 6.9 years ago • written 6.9 years ago by Pavel Senin1.9k
3
gravatar for Vitis
6.9 years ago by
Vitis2.3k
New York
Vitis2.3k wrote:

I would highly recommend Sequencher, but looks like its out of your preferences. I'd give 'cap3' a try. I have compared its results for EST clustering and assembly with Sequencher, and generally they perform relatively the same.

ADD COMMENTlink written 6.9 years ago by Vitis2.3k

+1 for CAP3; old but still good for this purpose.

ADD REPLYlink modified 6.9 years ago • written 6.9 years ago by Neilfws48k
2
gravatar for cts
6.9 years ago by
cts1.6k
Pasadena
cts1.6k wrote:

Well AMOS was developed to be open source and be used in situations where other assemblers are 'overkill'. Another option is MIRA which can handle everything from Sanger to Illumina

ADD COMMENTlink written 6.9 years ago by cts1.6k
1
gravatar for alessandro.riccombeni
6.9 years ago by
alessandro.riccombeni20 wrote:

In case somebody feels like trying it, I recommend giving Phred/Phrap a go, I used it 4 years ago and it was already ancient... and it worked great for assembling de novo Sanger data. Its usage is quite straightforward, probably the most complicated part is getting the licence via email.

ADD COMMENTlink written 6.9 years ago by alessandro.riccombeni20

That license is the sticking point though. I'd like to wrap the whole pipeline together and distribute it to the community at large, but the phred/phrap license won't allow that.

ADD REPLYlink written 6.9 years ago by Mike80
0
gravatar for BioApps
4.2 years ago by
BioApps740
Spain
BioApps740 wrote:

Here is one that is NOT freeware but it meets all other conditions of yours:

  • easy to use (non-overkill)
  • up to date
  • works on million of samples (your script only needs to provide the folders where your samples are)

This script demonstrates how easy it is to use:

BaserConsole.exe   /InputFolder=c:\samples    /FileType='*.abi'   
pause > nul
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by BioApps740
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