Question: Order of contigs
0
gravatar for agata88
2.4 years ago by
agata88800
Poland
agata88800 wrote:

Hi all!

I have 10 contigs presenting novel bacteria genome. How can I order them to fill gaps between with PCR?

Many thanks, Agata

contigs • 1000 views
ADD COMMENTlink modified 2.4 years ago by piet1.8k • written 2.4 years ago by agata88800
1
gravatar for Joe
2.4 years ago by
Joe18k
United Kingdom
Joe18k wrote:

Use progressiveMauve to order them relative to a reference.

ADD COMMENTlink written 2.4 years ago by Joe18k

Thanks. I don't have a reference. Should I use sequence of the closest related species?

ADD REPLYlink written 2.4 years ago by agata88800
1

Yeah that would probably be fine. Realistically you don’t necessarily need to re-order the contigs to close the gaps anyway. You can just design outward-looking primers to anneal to the end sequence you already have, and have it sequenced by Sanger sequencing.

Whatever you do, its probably going to be laborious though, since you don’t actually know how much missing sequence there is - those contigs are not going to connect directly to one another. I would suggest you look in to getting some Nanopore long read data to create a hybrid assembly.

ADD REPLYlink written 2.4 years ago by Joe18k

The genome size is close to related species, so I think I will be able to fill the gaps with Sanger. Thanks for your suggestions and answer.

ADD REPLYlink written 2.4 years ago by agata88800
0
gravatar for piet
2.4 years ago by
piet1.8k
planet earth
piet1.8k wrote:

You may inspect the *.gfa or *.fastg files (with bandage). That may give you some hints about putative linkages between contigs.

ADD COMMENTlink written 2.4 years ago by piet1.8k
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