Question: What is the best way to assemble Illumina paired end reads?
0
gravatar for Optimist
6 days ago by
Optimist130
Optimist130 wrote:

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

assembly sequencing illumina • 260 views
ADD COMMENTlink written 6 days ago by Optimist130
1

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.

ADD REPLYlink written 6 days ago by Mensur Dlakic8.1k

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.

ADD REPLYlink written 5 days ago by Optimist130
1
gravatar for shenwei356
6 days ago by
shenwei3565.7k
China
shenwei3565.7k wrote:

SPAdes, definitely.

ADD COMMENTlink written 6 days ago by shenwei3565.7k

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?

ADD REPLYlink written 5 days ago by Optimist130
1

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

ADD REPLYlink written 4 days ago by colindaven2.6k
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