Reads for assembly

Question

[glady]

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 ?

Answer 1

[lakhujanivijay]

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.

[glady]

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 ?