What is the best way to assemble Illumina paired end reads?

Question

[Optimist]

Hello Everyone,

Greetings!!

I would like to assemble my Bacterial genomes from Illumina paired end reads.

Can you all please help in figuring out the right tool and steps to do so.

Thanking You all

Cheers

[Mensur Dlakic]

Given the (lack of) information you have given us, it is the same as if you asked what is the best way to measure the square footage of a room. There are so many way to accomplish such a non-descript task that you will not be getting meaningful suggestions to your problem, but rather individual preferences for particular tools of those who answer.

[Optimist]

Thank You for your reply Sir. Apologies for the lack of information in my query.

I'm trying to assemble a bacterial genome using paired reads, sequenced using Illumina.
I want to know which assembler is best for this purpose.

Answer 1

[shenwei356]

SPAdes, definitely.

[Optimist]

Thank You for the response.

Can you share the best practices for a good assembly generation.

Commands and flags to be used for bacterial genome.

How to calculate depth or coverage of my reads?

[colindaven]

Maybe you should share more first, or show evidence of effort ? I second Spades, why don't you just try it ?