Question: Reads for assembly
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gravatar for glady
23 months ago by
glady240
glady240 wrote:

I want to experience myself, how do we assemble the raw read data of a genome obtained from sequencer. From where can I download the raw reads, for constructing assemble ?

assembly • 564 views
ADD COMMENTlink modified 23 months ago by Vijay Lakhujani4.1k • written 23 months ago by glady240
1
gravatar for Vijay Lakhujani
23 months ago by
Vijay Lakhujani4.1k
India
Vijay Lakhujani4.1k wrote:

I want to experience myself, how do we assemble the raw read data of a genome obtained from sequencer.

This is a very vague question. An assembly really depends on couple of factors like :

type of sequence - genome, transcriptome etc.

what species/organism it is - eukaryote/ prokaryote

whether the reference is available or not - denovo or reference based

platform - Illumina , pacbio etc.

Please include as much as possible information so that we can help you out.

From where can I download the raw reads, for constructing assemble ?

you can learn about SRA(Sequence Read Archive). Check out this detailed link about the same.

ADD COMMENTlink modified 23 months ago • written 23 months ago by Vijay Lakhujani4.1k

I want to download reads for a bacterial genome, it can be of any sequencing platform doesn't matter. From where I can download reads for it ? Any databases or links ? And how can we judge whether we have to go forward with a denovo assembly or a reference assembly ?

ADD REPLYlink written 23 months ago by glady240
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