Looking For A Good Open Source Command-Line Sanger Sequence Pairwise Assembler

Question

[Mike]

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!

[Pavel Senin]

I had good results with Arachne and Celera :)

Answer 1

[Vitis]

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.

[Neilfws]

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

Answer 2

[cts]

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

Answer 3

[alessandro.riccombeni]

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.

[Mike]

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.

Answer 4

[BioApps]

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