Re: [DIYbio] generate contigs from forward and reverse reads?

you could probably spin your own checkermerger with bioPython

On Thu, May 16, 2013 at 5:53 PM, Avery louie <inactive.e@gmail.com> wrote:
> Hey all,
>
> I am trying to generate some contiguous sequences from a forward and reverse
> read of the cloning site in pUC18 with m13 primers. Is there an easy way to
> do this?
>
> So far my approach has been to clustalo the the forward and antiparalell of
> the reverse sequences, but clustalo is not really good at this, as it tries
> to get the best fit where both sequences overlap the whole length of the
> sequence, like this:
>
> aaa---t---c---aa
> aaagctacccaa
>
> when really I want:
>
> aaatcaa---------------
> --------aaagctaccaa
>
> Let me know if you know the way!
>
> A
>
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--
-Nathan

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