General Category >> Help and How-to >> Sanger contig Assembly

Message started by Josh T on Oct 20th, 2022 at 10:21pm

Title: Sanger contig Assembly
Post by Josh T on Oct 20th, 2022 at 10:21pm
I've been scouring the website/forum for a few days now, while also dabbling with the program itself, but haven't gotten utility I need and was hoping someone could help.

I'm looking for something like Sequencher or Vector NTI that allows contig visualization of a forward and reverse output from 2 AB1 files. However, after contig I would like to edit any mismatches and trim primers/ends WHILE viewing 2 chromatograms stacked on each other. But I CANNOT use a reference sequence, as these are Unknown 16S region reads.

The closest I have gotten is using the CAP3, which automatically reverse/comp'd my reverse sequence... However, it doesn't look like the stacked chromatogram view that using a reference sequence appears.

Is there any feasible way of doing this properly, or has this not been implemented yet?  :'(
Thanks!  8-)

Title: Re: Sanger contig Assembly
Post by Dmitrii Sukhomlinov on Nov 14th, 2022 at 12:04pm

Sorry for a delayed answer. Unfortunately, we do not have a Sanger de novo assembly, you need to have a reference to assemble two reads from ab1 files. As a small trick, I can suggest you to use one of your ab1 files as a reference. If the second sequence (which is not reference) fits well to the first one, the will be assembled.

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